diff --git a/corelib/src/libs/SireMol/atommapping.cpp b/corelib/src/libs/SireMol/atommapping.cpp
index c38616017..5722d1de8 100644
--- a/corelib/src/libs/SireMol/atommapping.cpp
+++ b/corelib/src/libs/SireMol/atommapping.cpp
@@ -31,6 +31,7 @@
 #include "SireMaths/align.h"
 
 #include "SireMol/core.h"
+#include "SireMol/moleditor.h"
 
 #include "SireStream/datastream.h"
 #include "SireStream/shareddatastream.h"
@@ -723,20 +724,40 @@ AtomMapping AtomMapping::alignTo0() const
     QVector<Vector> coords0 = this->atms0.property<Vector>(map0["coordinates"]).toVector();
     QVector<Vector> coords1 = this->atms1.property<Vector>(map1["coordinates"]).toVector();
 
-    // calculate the transform to do a RMSD aligment of the two sets of coordinates
-    auto transform = SireMaths::getAlignment(coords0, coords1, true);
-
-    auto mols1 = this->orig_atms1.molecules();
-
     AtomMapping ret(*this);
 
-    for (int i = 0; i < mols1.count(); ++i)
+    if ((this->count() == 1) and ((coords0.count() == 1) or (coords1.count() == 1)))
     {
-        auto mol = mols1[i].move().transform(transform, map1).commit();
+        // if we've only mapped a single atom and one molecule is a monatomic ion,
+        // then simply replace the coordinates of the mapped atom.
+
+        auto atom0 = this->atms0[0];
+        auto atom1 = this->atms1[0];
+
+        auto mol = this->orig_atms1.molecules()[0];
+
+        mol = mol.edit().atom(atom1.index())
+                 .setProperty(map1["coordinates"].source(), coords0[0])
+                 .molecule().commit();
 
         ret.atms1.update(mol);
         ret.orig_atms1.update(mol);
     }
+    else
+    {
+        // calculate the transform to do a RMSD aligment of the two sets of coordinates
+        auto transform = SireMaths::getAlignment(coords0, coords1, true);
+
+        auto mols1 = this->orig_atms1.molecules();
+
+        for (int i = 0; i < mols1.count(); ++i)
+        {
+            auto mol = mols1[i].move().transform(transform, map1).commit();
+
+            ret.atms1.update(mol);
+            ret.orig_atms1.update(mol);
+        }
+    }
 
     return ret;
 }
@@ -754,20 +775,40 @@ AtomMapping AtomMapping::alignTo1() const
     QVector<Vector> coords0 = this->atms0.property<Vector>(map0["coordinates"]).toVector();
     QVector<Vector> coords1 = this->atms1.property<Vector>(map1["coordinates"]).toVector();
 
-    // calculate the transform to do a RMSD aligment of the two sets of coordinates
-    auto transform = SireMaths::getAlignment(coords1, coords0, true);
-
-    auto mols0 = this->orig_atms0.molecules();
-
     AtomMapping ret(*this);
 
-    for (int i = 0; i < mols0.count(); ++i)
+    if ((this->count() == 1) and ((coords0.count() == 1) or (coords1.count() == 1)))
     {
-        auto mol = mols0[i].move().transform(transform, map0).commit();
+        // if we've only mapped a single atom and one molecule is a monatomic ion,
+        // then simply replace the coordinates of the mapped atom.
+
+        auto atom0 = this->atms0[0];
+        auto atom1 = this->atms1[0];
+
+        auto mol = this->orig_atms0.molecules()[0];
+
+        mol = mol.edit().atom(atom0.index())
+                 .setProperty(map0["coordinates"].source(), coords0[0])
+                 .molecule().commit();
 
         ret.atms0.update(mol);
         ret.orig_atms0.update(mol);
     }
+    else
+    {
+        // calculate the transform to do a RMSD aligment of the two sets of coordinates
+        auto transform = SireMaths::getAlignment(coords1, coords0, true);
+
+        auto mols0 = this->orig_atms0.molecules();
+
+        for (int i = 0; i < mols0.count(); ++i)
+        {
+            auto mol = mols0[i].move().transform(transform, map0).commit();
+
+            ret.atms0.update(mol);
+            ret.orig_atms0.update(mol);
+        }
+    }
 
     return ret;
 }
diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
index cee9ded34..b55abf931 100644
--- a/doc/source/changelog.rst
+++ b/doc/source/changelog.rst
@@ -18,6 +18,7 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 * Please add an item to this changelog when you create your PR
 * Print residue indices of perturbed water molecules to SOMD1 log.
 * Add support for creating Na+ and Cl- ions.
+* Fix ``sire.morph.merge`` function when one molecule is a monatomic ion.
 
 `2024.2.0 <https://github.com/openbiosim/sire/compare/2024.1.0...2024.2.0>`__ - June 2024
 -----------------------------------------------------------------------------------------
diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py
index 8d5311569..238c4481f 100644
--- a/tests/morph/test_merge.py
+++ b/tests/morph/test_merge.py
@@ -202,3 +202,22 @@ def test_merge_neopentane_methane(neopentane_methane, openmm_platform):
     # These energies aren't correct - extra ghost atom internals?
     assert nrg_neo.value() == pytest.approx(nrg_merged_0.value(), abs=1e-3)
     # assert nrg_met.value() == pytest.approx(nrg_merged_1.value(), abs=1e-3)
+
+
+def test_ion_merge(ala_mols):
+    water = ala_mols[-1]
+    ion = sr.legacy.IO.createSodiumIon(water.atoms()[-1].coordinates(), "tip3p")
+
+    merged = sr.morph.merge(water, ion)
+
+    coords0 = merged.property("coordinates0").to_vector()[0]
+    coords1 = merged.property("coordinates1").to_vector()[0]
+
+    assert coords0 == coords1
+
+    merged = sr.morph.merge(ion, water)
+
+    coords0 = merged.property("coordinates0").to_vector()[0]
+    coords1 = merged.property("coordinates1").to_vector()[0]
+
+    assert coords0 == coords1