diff --git a/src/geom/SpanSet.cc b/src/geom/SpanSet.cc
index 6ec16ffdd..2a7512411 100644
--- a/src/geom/SpanSet.cc
+++ b/src/geom/SpanSet.cc
@@ -727,16 +727,18 @@ std::shared_ptr<SpanSet> SpanSet::intersect(SpanSet const& other) const {
         return std::make_shared<SpanSet>(this->_spanVector);
     }
     std::vector<Span> tempVec;
-    auto otherIter = other.begin();
+    auto otherBeginIter = other.begin();
     for (auto const& spn : _spanVector) {
-        while (otherIter != other.end() && otherIter->getY() <= spn.getY()) {
+        while(otherBeginIter != other.end() && otherBeginIter->getY() < spn.getY()) {
+            ++otherBeginIter;
+        }
+        for (auto otherIter = otherBeginIter; otherIter != other.end() && otherIter->getY() <= spn.getY(); ++otherIter) {
             if (spansOverlap(spn, *otherIter)) {
                 auto newMin = std::max(spn.getMinX(), otherIter->getMinX());
                 auto newMax = std::min(spn.getMaxX(), otherIter->getMaxX());
                 auto newSpan = Span(spn.getY(), newMin, newMax);
                 tempVec.push_back(newSpan);
             }
-            ++otherIter;
         }
     }
     return std::make_shared<SpanSet>(std::move(tempVec));
@@ -758,12 +760,15 @@ std::shared_ptr<SpanSet> SpanSet::intersectNot(SpanSet const& other) const {
      * or with other containing this  b1|    a1|    a2|   b2|
      */
     std::vector<Span> tempVec;
-    auto otherIter = other.begin();
+    auto otherBeginIter = other.begin();
     for (auto const& spn : _spanVector) {
         bool added = false;
         bool spanStarted = false;
         int spanBottom = 0;
-        while (otherIter != other.end() && otherIter->getY() <= spn.getY()) {
+        while(otherBeginIter != other.end() && otherBeginIter->getY() < spn.getY()) {
+            ++otherBeginIter;
+        }
+        for (auto otherIter = otherBeginIter; otherIter != other.end() && otherIter->getY() <= spn.getY(); ++otherIter) {
             if (spansOverlap(spn, *otherIter)) {
                 added = true;
                 /* To handle one span containing the other, the spans will be added
@@ -806,7 +811,6 @@ std::shared_ptr<SpanSet> SpanSet::intersectNot(SpanSet const& other) const {
             if (otherIter->getMaxX() > spn.getMaxX()) {
                 break;
             }
-            ++otherIter;
         }
         // Check if a span has been started but not finished, if that is the case that means there are
         // no further spans on this row to consider and the span should be closed and added
diff --git a/tests/test_spanSets.py b/tests/test_spanSets.py
index 79d1915de..e84a74ffe 100644
--- a/tests/test_spanSets.py
+++ b/tests/test_spanSets.py
@@ -252,6 +252,20 @@ def testIntersection(self):
         for expected, val in zip(expectedYRange, spanSetIntersectMask):
             self.assertEqual(expected, val.getY())
 
+    def testIntersectionWithGap(self):
+        # This test was created in DM-47945 to fix a bug where the
+        # intersection of two spansets where multiple spans have the same
+        # y-value would fail.
+        spans1 = afwGeom.SpanSet([afwGeom.Span(1, 0, 3), afwGeom.Span(1, 5, 7)])
+        spans2 = afwGeom.SpanSet([afwGeom.Span(1, 2, 6)])
+        intersection = spans1.intersect(spans2)
+        trueIntersection = afwGeom.SpanSet([afwGeom.Span(1, 2, 3), afwGeom.Span(1, 5, 6)])
+
+        self.assertEqual(len(intersection), 2)
+
+        for a, b in zip(intersection, trueIntersection):
+            self.assertEqual(a, b)
+
     def testIntersectNot(self):
         firstSpanSet, secondSpanSet = self.makeOverlapSpanSets()
 
@@ -322,6 +336,20 @@ def testIntersectNot(self):
                         targetSpanSet.contains(point):
                     self.assertTrue(resultSpanSet.contains(point))
 
+    def testIntersectNotWithGap(self):
+        # This test was created in DM-47945 to fix a bug where the
+        # intersection of two spansets where multiple spans have the same
+        # y-value would fail.
+        spans1 = afwGeom.SpanSet([afwGeom.Span(1, 0, 3), afwGeom.Span(1, 5, 7)])
+        spans2 = afwGeom.SpanSet([afwGeom.Span(1, 2, 6)])
+        intersectNot = spans1.intersectNot(spans2)
+        trueIntersectNot = afwGeom.SpanSet([afwGeom.Span(1, 0, 1), afwGeom.Span(1, 7, 7)])
+
+        self.assertEqual(len(intersectNot), 2)
+
+        for a, b in zip(intersectNot, trueIntersectNot):
+            self.assertEqual(a, b)
+
     def testUnion(self):
         firstSpanSet, secondSpanSet = self.makeOverlapSpanSets()