diff --git a/python/lsst/ip/diffim/detectAndMeasure.py b/python/lsst/ip/diffim/detectAndMeasure.py
index 0057fd47..7a2157f3 100644
--- a/python/lsst/ip/diffim/detectAndMeasure.py
+++ b/python/lsst/ip/diffim/detectAndMeasure.py
@@ -861,6 +861,9 @@ def processResults(self, science, matchedTemplate, difference, sources, idFactor
             initialDiaSources["is_negative"] = initialDiaSources["merge_footprint_negative"] & \
                 ~initialDiaSources["merge_footprint_positive"]
             self.log.info("Merging detections into %d sources", len(initialDiaSources))
+            # All positive peaks were added before any negative peaks, so
+            # re-order the peaks in each footprint by significance.
+            self._reorderPeaksBySignificance(initialDiaSources)
         else:
             initialDiaSources = sources
 
@@ -934,6 +937,24 @@ def processResults(self, science, matchedTemplate, difference, sources, idFactor
                       )
         return measurementResults
 
+    def _reorderPeaksBySignificance(self, diaSources):
+        """Sort each merged source's footprint peaks by significance.
+
+        Parameters
+        ----------
+        diaSources : `lsst.afw.table.SourceCatalog`
+            Merged sources whose footprint peaks are re-ordered in place.
+        """
+        for source in diaSources:
+            peaks = source.getFootprint().getPeaks()
+            if len(peaks) < 2 or "significance" not in peaks.schema.getNames():
+                continue
+            ordered = sorted(peaks, key=lambda peak: peak["significance"], reverse=True)
+            newPeaks = afwDetection.PeakCatalog(peaks.table)
+            newPeaks.extend(ordered)
+            peaks.clear()
+            source.getFootprint().setPeakCatalog(newPeaks)
+
     def _deblend(self, difference, positiveFootprints, negativeFootprints):
         """Deblend the positive and negative footprints and return a catalog
         containing just the children, and the deblended footprints.
diff --git a/tests/test_detectAndMeasure.py b/tests/test_detectAndMeasure.py
index ba1ba772..58315d35 100644
--- a/tests/test_detectAndMeasure.py
+++ b/tests/test_detectAndMeasure.py
@@ -25,8 +25,10 @@
 from unittest import mock
 import requests
 
+import lsst.afw.detection as afwDetection
 import lsst.afw.geom as afwGeom
 import lsst.afw.image as afwImage
+import lsst.afw.table as afwTable
 import lsst.afw.math as afwMath
 import lsst.geom
 from lsst.ip.diffim import detectAndMeasure, subtractImages
@@ -1500,6 +1502,41 @@ def testMergeFootprints(self):
         # handled.
         self.assertEqual((~result.diaSources["is_negative"]).sum(), 3)
 
+    def testReorderPeaksBySignificance(self):
+        """A merged footprint whose most significant peak is negative should
+        have that peak first after re-ordering, even though the merge lists
+        positive peaks before negative ones.
+        """
+        config = detectAndMeasure.DetectAndMeasureTask.ConfigClass()
+        task = detectAndMeasure.DetectAndMeasureTask(config=config)
+
+        # Peak schema with a significance field, as SourceDetectionTask
+        # produces for pixel_stdev thresholds.
+        mapper = afwTable.SchemaMapper(afwDetection.PeakTable.makeMinimalSchema())
+        mapper.addMinimalSchema(afwDetection.PeakTable.makeMinimalSchema())
+        mapper.addOutputField("significance", type=float, doc="")
+        peakSchema = mapper.getOutputSchema()
+
+        diaSources = afwTable.SourceCatalog(task.schema)
+        source = diaSources.addNew()
+        spans = afwGeom.SpanSet(geom.Box2I(geom.Point2I(0, 0), geom.Extent2I(10, 10)))
+        footprint = afwDetection.Footprint(spans, peakSchema)
+        # Merge order is [positive, negative]: a weak positive peak first,
+        # then a more significant negative peak.
+        footprint.addPeak(1, 1, 30.0)
+        footprint.peaks[-1]["significance"] = 5.0
+        footprint.addPeak(2, 2, -500.0)
+        footprint.peaks[-1]["significance"] = 40.0
+        source.setFootprint(footprint)
+
+        task._reorderPeaksBySignificance(diaSources)
+
+        peaks = source.getFootprint().peaks
+        self.assertEqual(peaks[0].getPeakValue(), -500.0)
+        self.assertEqual(peaks[0]["significance"], 40.0)
+        self.assertEqual(peaks[1].getPeakValue(), 30.0)
+        self.assertEqual(peaks[1]["significance"], 5.0)
+
 
 def makeVisitInfo(id=1):
     """Return a non-NaN visitInfo."""