diff --git a/packages/app/src/components/markdown/fence/mermaid/segments.ts b/packages/app/src/components/markdown/fence/mermaid/segments.ts
index dc21db3b1e..be2f229051 100644
--- a/packages/app/src/components/markdown/fence/mermaid/segments.ts
+++ b/packages/app/src/components/markdown/fence/mermaid/segments.ts
@@ -11,10 +11,11 @@ interface Segment {
 export function splitMermaidFences(markdown: string): Segment[] {
   if (!/mermaid/i.test(markdown)) return [{ kind: "markdown", id: "0", source: markdown }];
   const segments: Segment[] = [];
-  const definitions: Definition[] = [];
+  const definitions = new Map<string, Definition>();
   let cursor = 0;
   function visit(node: RootContent): void {
-    if (node.type === "definition") definitions.push(node);
+    if (node.type === "definition" && !definitions.has(node.identifier))
+      definitions.set(node.identifier, node);
     if (node.type === "code" && node.lang?.toLowerCase() === "mermaid" && node.position) {
       const start = node.position.start.offset!;
       const end = node.position.end.offset!;
@@ -36,9 +37,10 @@ export function splitMermaidFences(markdown: string): Segment[] {
       id: String(segments.length),
       source: markdown.slice(cursor),
     });
-  // Reference links keep their document-wide scope on both sides of a diagram.
+  // Prepend the document's first definitions after splitting, so fragment-local
+  // duplicates cannot override them. Original source slices and fence offsets stay intact.
   if (segments.some((segment) => segment.kind === "mermaid")) {
-    const referenceSource = definitions
+    const referenceSource = [...definitions.values()]
       .map((node) => {
         const label = node.identifier.replace(/[\\[\]]/g, "\\$&");
         const url = node.url.replace(/[\\<>]/g, "\\$&");
@@ -48,7 +50,7 @@ export function splitMermaidFences(markdown: string): Segment[] {
       .join("\n");
     if (referenceSource)
       for (const segment of segments) {
-        if (segment.kind === "markdown") segment.source += `\n\n${referenceSource}`;
+        if (segment.kind === "markdown") segment.source = `${referenceSource}\n\n${segment.source}`;
       }
   }
   return segments;
diff --git a/packages/app/src/components/markdown/renderer.test.ts b/packages/app/src/components/markdown/renderer.test.ts
index 560ae23973..9d47a2c65d 100644
--- a/packages/app/src/components/markdown/renderer.test.ts
+++ b/packages/app/src/components/markdown/renderer.test.ts
@@ -369,3 +369,25 @@ it("retries transient image decoding failures instead of caching an unavailable
   expect(attempts).toBe(2);
   client.clear();
 });
+
+it("keeps the document's first reference definition across every native Mermaid segment", async () => {
+  const { fromMarkdown } = await import("mdast-util-from-markdown");
+  const { splitMermaidFences } = await import("./fence/mermaid/segments");
+  const before = '[first]: /repo/first.ts "Original"\n\n';
+  const after = '\n\n[open][first]\n\n[first]: /repo/second.ts "Later"';
+  const source = `${before}\`\`\`mermaid\ngraph TD\nA-->B\n\`\`\`${after}`;
+  const firstDefinition = (markdown: string) =>
+    fromMarkdown(markdown).children.find((node) => node.type === "definition");
+  const canonical = firstDefinition(source);
+  const segments = splitMermaidFences(source);
+  for (const segment of segments.filter((candidate) => candidate.kind === "markdown")) {
+    expect(firstDefinition(segment.source)).toMatchObject({
+      identifier: canonical?.identifier,
+      url: canonical?.url,
+      title: canonical?.title,
+    });
+  }
+  expect(segments[0].source.endsWith(before)).toBe(true);
+  expect(segments[2].source.endsWith(after)).toBe(true);
+  expect(segments[1]).toEqual({ kind: "mermaid", id: "1", source: "graph TD\nA-->B" });
+});