diff --git a/packages/cli/src/acp/acpClient.ts b/packages/cli/src/acp/acpClient.ts
index db2d04dab4..ad796e6a9c 100644
--- a/packages/cli/src/acp/acpClient.ts
+++ b/packages/cli/src/acp/acpClient.ts
@@ -96,6 +96,8 @@ export async function runAcpClient(
   await connection.closed.finally(runExitCleanup);
 }
 
+let callIdCounter = 0;
+
 export class GeminiAgent {
   private sessions: Map<string, Session> = new Map();
   private clientCapabilities: acp.ClientCapabilities | undefined;
@@ -834,7 +836,7 @@ export class Session {
     promptId: string,
     fc: FunctionCall,
   ): Promise<Part[]> {
-    const callId = fc.id ?? `${fc.name}-${Date.now()}`;
+    const callId = fc.id ?? `${fc.name}-${Date.now()}-${++callIdCounter}`;
     const args = fc.args ?? {};
 
     const startTime = Date.now();
@@ -1295,7 +1297,7 @@ export class Session {
         include: pathSpecsToRead,
       };
 
-      const callId = `${readManyFilesTool.name}-${Date.now()}`;
+      const callId = `${readManyFilesTool.name}-${Date.now()}-${++callIdCounter}`;
 
       try {
         const invocation = readManyFilesTool.build(toolArgs);
diff --git a/packages/cli/src/ui/components/MainContent.test.tsx b/packages/cli/src/ui/components/MainContent.test.tsx
index e0880e624c..df80d93f1b 100644
--- a/packages/cli/src/ui/components/MainContent.test.tsx
+++ b/packages/cli/src/ui/components/MainContent.test.tsx
@@ -96,7 +96,7 @@ describe('getToolGroupBorderAppearance', () => {
   });
 
   it('inspects only the last pending tool_group item if current has no tools', () => {
-    const item = { type: 'tool_group' as const, tools: [], id: 1 };
+    const item = { type: 'tool_group' as const, tools: [], id: -1 };
     const pendingItems = [
       {
         type: 'tool_group' as const,
@@ -157,7 +157,7 @@ describe('getToolGroupBorderAppearance', () => {
           confirmationDetails: undefined,
         } as IndividualToolCallDisplay,
       ],
-      id: 1,
+      id: -1,
     };
     const result = getToolGroupBorderAppearance(
       item,
@@ -186,7 +186,7 @@ describe('getToolGroupBorderAppearance', () => {
           confirmationDetails: undefined,
         } as IndividualToolCallDisplay,
       ],
-      id: 1,
+      id: -1,
     };
     const result = getToolGroupBorderAppearance(
       item,
@@ -275,7 +275,7 @@ describe('getToolGroupBorderAppearance', () => {
           confirmationDetails: undefined,
         } as IndividualToolCallDisplay,
       ],
-      id: 1,
+      id: -1,
     };
     const result = getToolGroupBorderAppearance(
       item,
@@ -291,7 +291,7 @@ describe('getToolGroupBorderAppearance', () => {
   });
 
   it('handles empty tools with active shell turn (isCurrentlyInShellTurn)', () => {
-    const item = { type: 'tool_group' as const, tools: [], id: 1 };
+    const item = { type: 'tool_group' as const, tools: [], id: -1 };
 
     // active shell turn
     const result = getToolGroupBorderAppearance(
@@ -690,7 +690,7 @@ describe('MainContent', () => {
           pendingHistoryItems: [
             {
               type: 'tool_group',
-              id: 1,
+              id: -1,
               tools: [
                 {
                   callId: 'call_1',
diff --git a/packages/cli/src/ui/components/MainContent.tsx b/packages/cli/src/ui/components/MainContent.tsx
index d7e04bd351..8e0915a5cc 100644
--- a/packages/cli/src/ui/components/MainContent.tsx
+++ b/packages/cli/src/ui/components/MainContent.tsx
@@ -126,7 +126,7 @@ export const MainContent = () => {
 
   const pendingItems = useMemo(
     () => (
-      <Box flexDirection="column">
+      <Box flexDirection="column" key="pending-items-group">
         {pendingHistoryItems.map((item, i) => {
           const prevType =
             i === 0
@@ -139,12 +139,12 @@ export const MainContent = () => {
 
           return (
             <HistoryItemDisplay
-              key={i}
+              key={`pending-${i}`}
               availableTerminalHeight={
                 uiState.constrainHeight ? staticAreaMaxItemHeight : undefined
               }
               terminalWidth={mainAreaWidth}
-              item={{ ...item, id: 0 }}
+              item={{ ...item, id: -(i + 1) }}
               isPending={true}
               isExpandable={true}
               isFirstThinking={isFirstThinking}
@@ -153,7 +153,10 @@ export const MainContent = () => {
           );
         })}
         {showConfirmationQueue && confirmingTool && (
-          <ToolConfirmationQueue confirmingTool={confirmingTool} />
+          <ToolConfirmationQueue
+            key="confirmation-queue"
+            confirmingTool={confirmingTool}
+          />
         )}
       </Box>
     ),
diff --git a/packages/cli/src/ui/components/messages/DenseToolMessage.tsx b/packages/cli/src/ui/components/messages/DenseToolMessage.tsx
index 2751f4fd2c..359045719e 100644
--- a/packages/cli/src/ui/components/messages/DenseToolMessage.tsx
+++ b/packages/cli/src/ui/components/messages/DenseToolMessage.tsx
@@ -519,12 +519,12 @@ export const DenseToolMessage: React.FC<DenseToolMessageProps> = (props) => {
           {description}
         </Box>
         {summary && (
-          <Box marginLeft={1} flexGrow={0}>
+          <Box key="tool-summary" marginLeft={1} flexGrow={0}>
             {summary}
           </Box>
         )}
         {isAlternateBuffer && diff && (
-          <Box ref={toggleRef} marginLeft={1} flexGrow={1}>
+          <Box key="tool-toggle" ref={toggleRef} marginLeft={1} flexGrow={1}>
             <Text color={theme.text.link} dimColor>
               [{isExpanded ? 'Hide Diff' : 'Show Diff'}]
             </Text>
diff --git a/packages/cli/src/ui/hooks/useHistoryManager.test.ts b/packages/cli/src/ui/hooks/useHistoryManager.test.ts
index 696f9d60c0..b657e5d4ba 100644
--- a/packages/cli/src/ui/hooks/useHistoryManager.test.ts
+++ b/packages/cli/src/ui/hooks/useHistoryManager.test.ts
@@ -39,6 +39,56 @@ describe('useHistoryManager', () => {
     expect(result.current.history[0].id).toBeGreaterThanOrEqual(timestamp);
   });
 
+  it('should generate strictly increasing IDs even if baseTimestamp goes backwards', () => {
+    const { result } = renderHook(() => useHistory());
+    const timestamp = 1000000;
+    const itemData: Omit<HistoryItem, 'id'> = { type: 'info', text: 'First' };
+
+    let id1!: number;
+    let id2!: number;
+
+    act(() => {
+      id1 = result.current.addItem(itemData, timestamp);
+      // Try to add with a smaller timestamp
+      id2 = result.current.addItem(itemData, timestamp - 500);
+    });
+
+    expect(id1).toBe(timestamp);
+    expect(id2).toBe(id1 + 1);
+    expect(result.current.history[1].id).toBe(id2);
+  });
+
+  it('should ensure new IDs start after existing IDs when resuming a session', () => {
+    const initialItems: HistoryItem[] = [
+      { id: 5000, type: 'info', text: 'Existing' },
+    ];
+    const { result } = renderHook(() => useHistory({ initialItems }));
+
+    let newId!: number;
+    act(() => {
+      // Try to add with a timestamp smaller than the highest existing ID
+      newId = result.current.addItem({ type: 'info', text: 'New' }, 2000);
+    });
+
+    expect(newId).toBe(5001);
+    expect(result.current.history[1].id).toBe(5001);
+  });
+
+  it('should update lastIdRef when loading new history', () => {
+    const { result } = renderHook(() => useHistory());
+
+    act(() => {
+      result.current.loadHistory([{ id: 8000, type: 'info', text: 'Loaded' }]);
+    });
+
+    let newId!: number;
+    act(() => {
+      newId = result.current.addItem({ type: 'info', text: 'New' }, 1000);
+    });
+
+    expect(newId).toBe(8001);
+  });
+
   it('should generate unique IDs for items added with the same base timestamp', () => {
     const { result } = renderHook(() => useHistory());
     const timestamp = Date.now();
@@ -215,8 +265,8 @@ describe('useHistoryManager', () => {
     const after = Date.now();
 
     expect(result.current.history).toHaveLength(1);
-    // ID should be >= before + 1 (since counter starts at 0 and increments to 1)
-    expect(result.current.history[0].id).toBeGreaterThanOrEqual(before + 1);
+    // ID should be >= before (since baseTimestamp defaults to Date.now())
+    expect(result.current.history[0].id).toBeGreaterThanOrEqual(before);
     expect(result.current.history[0].id).toBeLessThanOrEqual(after + 1);
   });
 
diff --git a/packages/cli/src/ui/hooks/useHistoryManager.ts b/packages/cli/src/ui/hooks/useHistoryManager.ts
index 93f7f01f28..c6ceabb920 100644
--- a/packages/cli/src/ui/hooks/useHistoryManager.ts
+++ b/packages/cli/src/ui/hooks/useHistoryManager.ts
@@ -42,16 +42,22 @@ export function useHistory({
   initialItems?: HistoryItem[];
 } = {}): UseHistoryManagerReturn {
   const [history, setHistory] = useState<HistoryItem[]>(initialItems);
-  const messageIdCounterRef = useRef(0);
+  const lastIdRef = useRef(
+    initialItems.reduce((max, item) => Math.max(max, item.id), 0),
+  );
 
-  // Generates a unique message ID based on a timestamp and a counter.
+  // Generates a unique message ID based on a timestamp, ensuring it is always
+  // greater than any previously assigned ID.
   const getNextMessageId = useCallback((baseTimestamp: number): number => {
-    messageIdCounterRef.current += 1;
-    return baseTimestamp + messageIdCounterRef.current;
+    const nextId = Math.max(baseTimestamp, lastIdRef.current + 1);
+    lastIdRef.current = nextId;
+    return nextId;
   }, []);
 
   const loadHistory = useCallback((newHistory: HistoryItem[]) => {
     setHistory(newHistory);
+    const maxId = newHistory.reduce((max, item) => Math.max(max, item.id), 0);
+    lastIdRef.current = Math.max(lastIdRef.current, maxId);
   }, []);
 
   // Adds a new item to the history state with a unique ID.
@@ -153,7 +159,7 @@ export function useHistory({
   // Clears the entire history state and resets the ID counter.
   const clearItems = useCallback(() => {
     setHistory([]);
-    messageIdCounterRef.current = 0;
+    lastIdRef.current = 0;
   }, []);
 
   return useMemo(