diff --git a/src/connectors/obsidian.ts b/src/connectors/obsidian.ts
index 9739c5e..00a8d83 100644
--- a/src/connectors/obsidian.ts
+++ b/src/connectors/obsidian.ts
@@ -7,6 +7,7 @@ import { indexDocument } from "../core/indexing.js";
 import { deleteDocument } from "../core/documents.js";
 import { createTopic, listTopics } from "../core/topics.js";
 import { addTagsToDocument, createTag } from "../core/tags.js";
+import { createLink, resolveDocumentByTitle } from "../core/links.js";
 import { getLogger } from "../logger.js";
 import { ValidationError } from "../errors.js";
 import { loadConnectorConfig, saveConnectorConfig } from "./index.js";
@@ -357,6 +358,20 @@ export async function syncObsidianVault(
           }
         }
 
+        // Store wikilinks as document references
+        if (parsed.wikilinks.length > 0) {
+          for (const pageName of parsed.wikilinks) {
+            try {
+              const targetId = resolveDocumentByTitle(db, pageName);
+              if (targetId && targetId !== indexed.id) {
+                createLink(db, indexed.id, targetId, "references");
+              }
+            } catch (err) {
+              log.debug({ err, pageName, docId: indexed.id }, "Failed to resolve wikilink");
+            }
+          }
+        }
+
         newTrackedFiles[relPath] = { mtime, docId: indexed.id };
 
         if (tracked) {
diff --git a/src/core/graph.ts b/src/core/graph.ts
index a385d04..1f4b89c 100644
--- a/src/core/graph.ts
+++ b/src/core/graph.ts
@@ -11,7 +11,15 @@ export interface GraphNode {
 export interface GraphEdge {
   source: string;
   target: string;
-  type: "belongs_to_topic" | "has_tag" | "similar_to";
+  type:
+    | "belongs_to_topic"
+    | "has_tag"
+    | "similar_to"
+    | "see_also"
+    | "prerequisite"
+    | "supersedes"
+    | "related"
+    | "references";
   weight: number; // 0-1
 }
 
@@ -196,6 +204,22 @@ export function buildKnowledgeGraph(
     }
   }
 
+  // Add document link edges
+  const docLinks = db
+    .prepare("SELECT source_id, target_id, link_type FROM document_links")
+    .all() as Array<{ source_id: string; target_id: string; link_type: string }>;
+
+  for (const link of docLinks) {
+    if (docIds.has(link.source_id) && docIds.has(link.target_id)) {
+      edges.push({
+        source: link.source_id,
+        target: link.target_id,
+        type: link.link_type as GraphEdge["type"],
+        weight: 1,
+      });
+    }
+  }
+
   // Compute similarity edges from chunk embeddings
   if (includeSimilarity && documents.length > 1) {
     try {
diff --git a/src/core/indexing.ts b/src/core/indexing.ts
index 2a025d5..0f1a015 100644
--- a/src/core/indexing.ts
+++ b/src/core/indexing.ts
@@ -8,6 +8,7 @@ import { ValidationError } from "../errors.js";
 import { getLogger } from "../logger.js";
 import { checkDuplicate } from "./dedup.js";
 import type { DedupOptions } from "./dedup.js";
+import { extractAndStoreDocumentLinks } from "./links.js";
 import { getParserForFile, getSupportedExtensions } from "./parsers/index.js";
 
 export interface IndexDocumentInput {
@@ -470,6 +471,14 @@ export async function indexDocument(
   transaction();
 
   log.info({ docId, chunkCount: chunks.length }, "Document indexed successfully");
+
+  // Extract and store document links (best-effort — don't fail indexing)
+  try {
+    extractAndStoreDocumentLinks(db, docId, input.content);
+  } catch (err) {
+    log.warn({ err, docId }, "Failed to extract document links");
+  }
+
   return { id: docId, chunkCount: chunks.length };
 }
 
diff --git a/src/core/link-extractor.ts b/src/core/link-extractor.ts
index 5c7c889..ed6e59f 100644
--- a/src/core/link-extractor.ts
+++ b/src/core/link-extractor.ts
@@ -127,6 +127,46 @@ function extractHref(tag: string): string | null {
  * Resolve a potentially-relative href against a base URL.
  * Returns null if the result is not an http/https URL (e.g. mailto:, javascript:, data:, #fragment-only).
  */
+/**
+ * Extract markdown-style links from content.
+ * Parses [text](url) patterns and returns an array of {text, url} objects.
+ */
+export function extractMarkdownLinks(content: string): Array<{ text: string; url: string }> {
+  if (!content) return [];
+
+  const results: Array<{ text: string; url: string }> = [];
+  const re = /\[([^\]]*)\]\(([^)]+)\)/g;
+  let match: RegExpExecArray | null;
+
+  while ((match = re.exec(content)) !== null) {
+    results.push({ text: match[1]!, url: match[2]! });
+  }
+
+  return results;
+}
+
+/**
+ * Extract wikilinks from content.
+ * Parses [[PageName]] and [[PageName|alias]] formats.
+ * Returns deduplicated array of page names.
+ */
+export function extractWikilinks(content: string): string[] {
+  if (!content) return [];
+
+  const seen = new Set<string>();
+  const re = /\[\[([^\]|]+)(?:\|[^\]]+)?\]\]/g;
+  let match: RegExpExecArray | null;
+
+  while ((match = re.exec(content)) !== null) {
+    const pageName = match[1]!.trim();
+    if (pageName) {
+      seen.add(pageName);
+    }
+  }
+
+  return [...seen];
+}
+
 function resolveUrl(href: string, baseUrl: string): string | null {
   // Skip fragment-only links immediately — they point to the same page
   if (href.startsWith("#")) return null;
diff --git a/src/core/links.ts b/src/core/links.ts
index 673c801..e725d71 100644
--- a/src/core/links.ts
+++ b/src/core/links.ts
@@ -2,14 +2,16 @@ import type Database from "better-sqlite3";
 import { randomUUID } from "node:crypto";
 import { ValidationError, DocumentNotFoundError } from "../errors.js";
 import { createChildLogger } from "../logger.js";
+import { extractMarkdownLinks, extractWikilinks } from "./link-extractor.js";
 
-export type LinkType = "see_also" | "prerequisite" | "supersedes" | "related";
+export type LinkType = "see_also" | "prerequisite" | "supersedes" | "related" | "references";
 
 const VALID_LINK_TYPES: ReadonlySet<string> = new Set<LinkType>([
   "see_also",
   "prerequisite",
   "supersedes",
   "related",
+  "references",
 ]);
 
 export interface DocumentLink {
@@ -224,3 +226,56 @@ export function listLinks(db: Database.Database, linkType?: LinkType): DocumentL
   const rows = db.prepare(sql).all(...params) as LinkRowWithTitles[];
   return rows.map(rowToLinkWithTitle);
 }
+
+/** Resolve a document by its URL. Returns the document id or null. */
+export function resolveDocumentByUrl(db: Database.Database, url: string): string | null {
+  const row = db.prepare("SELECT id FROM documents WHERE url = ? LIMIT 1").get(url) as
+    | { id: string }
+    | undefined;
+  return row?.id ?? null;
+}
+
+/** Resolve a document by its title (case-insensitive). Returns the document id or null. */
+export function resolveDocumentByTitle(db: Database.Database, title: string): string | null {
+  const row = db
+    .prepare("SELECT id FROM documents WHERE lower(title) = lower(?) LIMIT 1")
+    .get(title) as { id: string } | undefined;
+  return row?.id ?? null;
+}
+
+/** Resolve a document reference by trying URL first, then title. Returns the document id or null. */
+export function resolveDocumentLink(db: Database.Database, ref: string): string | null {
+  return resolveDocumentByUrl(db, ref) ?? resolveDocumentByTitle(db, ref);
+}
+
+/** Extract markdown and wiki links from content, resolve them, and store as "references" links. */
+export function extractAndStoreDocumentLinks(
+  db: Database.Database,
+  documentId: string,
+  content: string,
+): void {
+  const log = createChildLogger({ operation: "extractAndStoreDocumentLinks" });
+  const resolved = new Set<string>();
+
+  for (const { url } of extractMarkdownLinks(content)) {
+    const targetId = resolveDocumentLink(db, url);
+    if (targetId && targetId !== documentId) {
+      resolved.add(targetId);
+    }
+  }
+
+  for (const pageName of extractWikilinks(content)) {
+    const targetId = resolveDocumentLink(db, pageName);
+    if (targetId && targetId !== documentId) {
+      resolved.add(targetId);
+    }
+  }
+
+  for (const targetId of resolved) {
+    try {
+      createLink(db, documentId, targetId, "references");
+    } catch (e) {
+      log.warn({ documentId, targetId, error: e }, "Failed to create reference link, skipping");
+    }
+  }
+}
diff --git a/tests/unit/document-links-resolution.test.ts b/tests/unit/document-links-resolution.test.ts
new file mode 100644
index 0000000..8ff560a
--- /dev/null
+++ b/tests/unit/document-links-resolution.test.ts
@@ -0,0 +1,109 @@
+import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import type Database from "better-sqlite3";
+import { createTestDb } from "../fixtures/test-db.js";
+import {
+  resolveDocumentByUrl,
+  resolveDocumentByTitle,
+  resolveDocumentLink,
+  extractAndStoreDocumentLinks,
+  getDocumentLinks,
+} from "../../src/core/links.js";
+
+function insertDocWithUrl(
+  db: Database.Database,
+  id: string,
+  title: string,
+  url: string | null,
+): void {
+  db.prepare(
+    `INSERT INTO documents (id, title, content, source_type, url) VALUES (?, ?, '', 'manual', ?)`,
+  ).run(id, title, url);
+}
+
+describe("document link resolution", () => {
+  let db: Database.Database;
+
+  beforeEach(() => {
+    db = createTestDb();
+    insertDocWithUrl(db, "doc-a", "Document A", "https://example.com/a");
+    insertDocWithUrl(db, "doc-b", "Document B", "https://example.com/b");
+    insertDocWithUrl(db, "doc-c", "Document C", null);
+  });
+
+  afterEach(() => {
+    db.close();
+  });
+
+  describe("resolveDocumentByUrl", () => {
+    it("should return document id for existing URL", () => {
+      expect(resolveDocumentByUrl(db, "https://example.com/a")).toBe("doc-a");
+    });
+
+    it("should return null for nonexistent URL", () => {
+      expect(resolveDocumentByUrl(db, "https://example.com/missing")).toBeNull();
+    });
+  });
+
+  describe("resolveDocumentByTitle", () => {
+    it("should match case-insensitively", () => {
+      expect(resolveDocumentByTitle(db, "document a")).toBe("doc-a");
+      expect(resolveDocumentByTitle(db, "DOCUMENT B")).toBe("doc-b");
+    });
+
+    it("should return null when no match", () => {
+      expect(resolveDocumentByTitle(db, "Nonexistent Doc")).toBeNull();
+    });
+  });
+
+  describe("resolveDocumentLink", () => {
+    it("should resolve by URL first", () => {
+      expect(resolveDocumentLink(db, "https://example.com/a")).toBe("doc-a");
+    });
+
+    it("should fall back to title when URL does not match", () => {
+      expect(resolveDocumentLink(db, "Document C")).toBe("doc-c");
+    });
+
+    it("should return null if neither URL nor title matches", () => {
+      expect(resolveDocumentLink(db, "nothing matches")).toBeNull();
+    });
+  });
+
+  describe("extractAndStoreDocumentLinks", () => {
+    it("should create references links for resolvable markdown refs", () => {
+      const content = "See [Doc B](https://example.com/b) for more.";
+      extractAndStoreDocumentLinks(db, "doc-a", content);
+
+      const { outgoing } = getDocumentLinks(db, "doc-a");
+      expect(outgoing).toHaveLength(1);
+      expect(outgoing[0]!.targetId).toBe("doc-b");
+      expect(outgoing[0]!.linkType).toBe("references");
+    });
+
+    it("should create references links for resolvable wikilinks", () => {
+      const content = "See [[Document B]] for more.";
+      extractAndStoreDocumentLinks(db, "doc-a", content);
+
+      const { outgoing } = getDocumentLinks(db, "doc-a");
+      expect(outgoing).toHaveLength(1);
+      expect(outgoing[0]!.targetId).toBe("doc-b");
+      expect(outgoing[0]!.linkType).toBe("references");
+    });
+
+    it("should skip unresolvable references", () => {
+      const content = "See [missing](https://example.com/missing) and [[Unknown Page]].";
+      extractAndStoreDocumentLinks(db, "doc-a", content);
+
+      const { outgoing } = getDocumentLinks(db, "doc-a");
+      expect(outgoing).toHaveLength(0);
+    });
+
+    it("should skip self-links", () => {
+      const content = "See [self](https://example.com/a).";
+      extractAndStoreDocumentLinks(db, "doc-a", content);
+
+      const { outgoing } = getDocumentLinks(db, "doc-a");
+      expect(outgoing).toHaveLength(0);
+    });
+  });
+});
diff --git a/tests/unit/graph-document-links.test.ts b/tests/unit/graph-document-links.test.ts
new file mode 100644
index 0000000..f3fb44b
--- /dev/null
+++ b/tests/unit/graph-document-links.test.ts
@@ -0,0 +1,33 @@
+import { describe, it, expect, beforeEach } from "vitest";
+import type Database from "better-sqlite3";
+import { createTestDb } from "../fixtures/test-db.js";
+import { buildKnowledgeGraph } from "../../src/core/graph.js";
+import { createLink } from "../../src/core/links.js";
+
+function insertDocument(db: Database.Database, id: string, title: string): void {
+  db.prepare(
+    `INSERT INTO documents (id, source_type, title, content) VALUES (?, 'manual', ?, 'content')`,
+  ).run(id, title);
+}
+
+describe("buildKnowledgeGraph with document_links", () => {
+  let db: Database.Database;
+
+  beforeEach(() => {
+    db = createTestDb();
+  });
+
+  it("should include document_links edges with type references", async () => {
+    insertDocument(db, "d1", "Doc One");
+    insertDocument(db, "d2", "Doc Two");
+    createLink(db, "d1", "d2", "references");
+
+    const graph = await buildKnowledgeGraph(db, { includeSimilarityEdges: false });
+
+    const refEdges = graph.edges.filter((e) => e.type === "references");
+    expect(refEdges).toHaveLength(1);
+    expect(refEdges[0]!.source).toBe("d1");
+    expect(refEdges[0]!.target).toBe("d2");
+    expect(refEdges[0]!.weight).toBe(1);
+  });
+});
diff --git a/tests/unit/link-extractor.test.ts b/tests/unit/link-extractor.test.ts
index f623eba..c6731f7 100644
--- a/tests/unit/link-extractor.test.ts
+++ b/tests/unit/link-extractor.test.ts
@@ -1,5 +1,9 @@
 import { describe, it, expect } from "vitest";
-import { extractLinks } from "../../src/core/link-extractor.js";
+import {
+  extractLinks,
+  extractMarkdownLinks,
+  extractWikilinks,
+} from "../../src/core/link-extractor.js";
 
 const BASE = "https://example.com/docs/intro";
 
@@ -153,3 +157,45 @@ describe("extractLinks", () => {
     expect(links).toContain("https://example.com/https");
   });
 });
+
+describe("extractMarkdownLinks", () => {
+  it("extracts a standard markdown link", () => {
+    const result = extractMarkdownLinks("[click here](https://example.com)");
+    expect(result).toEqual([{ text: "click here", url: "https://example.com" }]);
+  });
+
+  it("extracts multiple links", () => {
+    const content = "See [a](https://a.com) and [b](https://b.com).";
+    const result = extractMarkdownLinks(content);
+    expect(result).toHaveLength(2);
+    expect(result[0]).toEqual({ text: "a", url: "https://a.com" });
+    expect(result[1]).toEqual({ text: "b", url: "https://b.com" });
+  });
+
+  it("returns empty array when no links present", () => {
+    expect(extractMarkdownLinks("no links here")).toEqual([]);
+  });
+
+  it("returns empty array for empty string", () => {
+    expect(extractMarkdownLinks("")).toEqual([]);
+  });
+});
+
+describe("extractWikilinks", () => {
+  it("extracts a simple wikilink", () => {
+    expect(extractWikilinks("See [[MyPage]] for details")).toEqual(["MyPage"]);
+  });
+
+  it("extracts page name from aliased wikilink, not the alias", () => {
+    expect(extractWikilinks("See [[MyPage|display text]]")).toEqual(["MyPage"]);
+  });
+
+  it("extracts multiple wikilinks and deduplicates", () => {
+    const result = extractWikilinks("[[A]] then [[B]] then [[A]] again");
+    expect(result).toEqual(["A", "B"]);
+  });
+
+  it("returns empty array for empty string", () => {
+    expect(extractWikilinks("")).toEqual([]);
+  });
+});