diff --git a/scripts/pr_queue_health.py b/scripts/pr_queue_health.py
index e96ed86d..4eafcc5a 100644
--- a/scripts/pr_queue_health.py
+++ b/scripts/pr_queue_health.py
@@ -8,7 +8,11 @@
 from collections import defaultdict
 from typing import Any
 
-BOUNTY_REF_RE = re.compile(r"\b(?:bounty|refs?|fixes|closes|claims?)\s+#(\d+)", re.IGNORECASE)
+BOUNTY_REF_RE = re.compile(
+    r"\b(?:(?P<native_prefix>live|mrwk|native|internal)\s+)?"
+    r"(?P<keyword>bounty|issues?|refs?|fixes|closes|claims?)\s+#(?P<number>\d+)",
+    re.IGNORECASE,
+)
 NOISY_TITLE_PREFIX_RE = re.compile(r"^\s*(?:\[[^\]]+\]\s*)+")
 UNSTABLE_MERGE_STATES = {"blocked", "conflicting", "dirty", "unknown", "unstable"}
 GH_TIMEOUT_SECONDS = 30
@@ -47,15 +51,22 @@ def _scope_key(raw: dict[str, Any]) -> str:
 def _bounty_refs(raw: dict[str, Any]) -> list[int]:
     explicit = raw.get("bounty_refs")
     if isinstance(explicit, list):
-        refs = [item for item in explicit if isinstance(item, int)]
-        if refs:
-            return sorted(set(refs))
+        explicit_refs = [
+            item for item in explicit if isinstance(item, int) and not isinstance(item, bool)
+        ]
+        if explicit_refs:
+            return sorted(set(explicit_refs))
     text = "\n".join(
         str(raw.get(key) or "")
         for key in ("title", "body", "description")
         if raw.get(key) is not None
     )
-    return sorted({int(match) for match in BOUNTY_REF_RE.findall(text)})
+    refs: set[int] = set()
+    for match in BOUNTY_REF_RE.finditer(text):
+        if match.group("native_prefix") and match.group("keyword").lower() == "bounty":
+            continue
+        refs.add(int(match.group("number")))
+    return sorted(refs)
 
 
 def _is_open_bounty(raw: dict[str, Any]) -> bool:
@@ -116,7 +127,7 @@ def analyze_queue(data: dict[str, Any]) -> dict[str, Any]:
                 _issue(
                     pr,
                     "missing_bounty_reference",
-                    "No Bounty #<issue>, Refs #<issue>, or /claim #<issue> found",
+                    "No Bounty #<issue>, Issue #<issue>, Refs #<issue>, or /claim #<issue> found",
                 )
             )
         for ref in pr["refs"]:
diff --git a/tests/test_pr_queue_health.py b/tests/test_pr_queue_health.py
index 58ff8fbe..67be0ece 100644
--- a/tests/test_pr_queue_health.py
+++ b/tests/test_pr_queue_health.py
@@ -127,6 +127,120 @@ def test_pr_queue_health_accepts_claim_command_reference() -> None:
     assert report["missing_bounty_references"] == []
 
 
+def test_pr_queue_health_ignores_boolean_explicit_bounty_refs() -> None:
+    report = analyze_queue(
+        {
+            "bounties": [{"number": 406, "state": "OPEN", "awards_remaining": 1}],
+            "pull_requests": [
+                {
+                    "number": 531,
+                    "title": "Boolean refs are not issue refs",
+                    "body": "",
+                    "bounty_refs": [True, False],
+                    "merge_state": "clean",
+                    "labels": [],
+                },
+                {
+                    "number": 532,
+                    "title": "Valid explicit issue ref still counts",
+                    "body": "",
+                    "bounty_refs": [True, 406],
+                    "merge_state": "clean",
+                    "labels": [],
+                },
+            ],
+        }
+    )
+
+    assert report["summary"]["missing_bounty_references"] == 1
+    assert report["missing_bounty_references"][0]["pull_request"] == 531
+    assert report["closed_bounty_references"] == []
+
+
+def test_pr_queue_health_ignores_native_bounty_ids_when_issue_ref_is_present() -> None:
+    report = analyze_queue(
+        {
+            "bounties": [{"number": 406, "state": "OPEN", "awards_remaining": 16}],
+            "pull_requests": [
+                {
+                    "number": 524,
+                    "title": "Refs #406: Reject malformed IPv4 public URLs",
+                    "body": (
+                        "Focused #406 small fix. Evidence: live bounty #66 / issue #406 "
+                        "preflight returned status=open."
+                    ),
+                    "merge_state": "clean",
+                    "labels": [],
+                },
+                {
+                    "number": 525,
+                    "title": "Guard another #406 edge case",
+                    "body": "MRWK bounty #66 maps to issue #406.",
+                    "merge_state": "clean",
+                    "labels": [],
+                },
+                {
+                    "number": 528,
+                    "title": "Ignore spaced live bounty evidence ids",
+                    "body": (
+                        "Evidence: live  bounty #66 and live\tbounty #67 both map to issue #406."
+                    ),
+                    "merge_state": "clean",
+                    "labels": [],
+                },
+                {
+                    "number": 526,
+                    "title": "Ignore native #406 evidence ids",
+                    "body": (
+                        "Evidence: native bounty #66 / issue #406 preflight returned status=open."
+                    ),
+                    "merge_state": "clean",
+                    "labels": [],
+                },
+                {
+                    "number": 527,
+                    "title": "Ignore internal #406 evidence ids",
+                    "body": "Evidence: internal bounty #66, issue #406 is the GitHub bounty.",
+                    "merge_state": "clean",
+                    "labels": [],
+                },
+            ],
+        }
+    )
+
+    assert report["summary"]["closed_bounty_references"] == 0
+    assert report["summary"]["missing_bounty_references"] == 0
+    assert report["closed_bounty_references"] == []
+    assert report["missing_bounty_references"] == []
+
+
+def test_pr_queue_health_requires_issue_ref_when_only_native_bounty_id_is_present() -> None:
+    report = analyze_queue(
+        {
+            "bounties": [{"number": 406, "state": "OPEN", "awards_remaining": 16}],
+            "pull_requests": [
+                {
+                    "number": 529,
+                    "title": "Needs GitHub issue reference",
+                    "body": "Evidence: live bounty #66 returned status=open.",
+                    "merge_state": "clean",
+                    "labels": [],
+                },
+                {
+                    "number": 530,
+                    "title": "Longer words still count as bounty refs",
+                    "body": "Evidence: relive bounty #406 returned status=open.",
+                    "merge_state": "clean",
+                    "labels": [],
+                },
+            ],
+        }
+    )
+
+    assert report["summary"]["missing_bounty_references"] == 1
+    assert report["missing_bounty_references"][0]["pull_request"] == 529
+
+
 def test_pr_queue_health_markdown_report_includes_required_sections() -> None:
     report = analyze_queue(
         {
@@ -183,7 +297,8 @@ def test_pr_queue_health_markdown_report_includes_required_sections() -> None:
     assert "### Missing bounty references" in markdown
     assert (
         "- [PR #2](https://github.com/ramimbo/mergework/pull/2): "
-        "Improve bounty filters (No Bounty #<issue>, Refs #<issue>, or /claim #<issue> found)"
+        "Improve bounty filters "
+        "(No Bounty #<issue>, Issue #<issue>, Refs #<issue>, or /claim #<issue> found)"
     ) in markdown
     assert "### Dirty or unstable merge state" in markdown
     assert "Merge state is dirty" in markdown