diff --git a/src/main/org/openscience/cdk/similarity/Tanimoto.java b/src/main/org/openscience/cdk/similarity/Tanimoto.java
index 9bb63c773a5..6397b172dc8 100644
--- a/src/main/org/openscience/cdk/similarity/Tanimoto.java
+++ b/src/main/org/openscience/cdk/similarity/Tanimoto.java
@@ -225,23 +225,27 @@ public static float method2( ICountFingerprint fp1,
     		    j = 0;
     		while ( i < fp1.numOfPopulatedbins() 
     				|| j < fp2.numOfPopulatedbins() ) {
-    			int hash1 = fp1.getHash(i);
-    			int hash2 = fp2.getHash(j);
-			int count1 = fp1.getCount(i);
-			int count2 = fp2.getCount(j);
+    			Integer hash1 = i < fp1.numOfPopulatedbins() ? fp1.getHash(i) 
+    					                                     : null;
+    			Integer hash2 = j < fp2.numOfPopulatedbins() ? fp2.getHash(j) 
+    					                                     : null;
+			Integer count1 = i < fp1.numOfPopulatedbins() ? fp1.getCount(i) 
+					                                      : null;
+			Integer count2 = j < fp2.numOfPopulatedbins() ? fp2.getCount(j) 
+					                                      : null;
     			
-    			if ( hash1 < hash2) {
+    			if ( count2 == null || (hash1 != null && hash1 < hash2) ) {
 				maxSum += count1;
     				i++;
     				continue;
     			}
-    			if ( hash1 > hash2 ) {
+    			if ( count1 == null || (hash2 != null && hash1 > hash2 ) ) {
     				maxSum += count2;
     				j++;
     				continue;
     			}
     			
-    			if ( hash1 == hash2 ) {
+    			if ( hash1.equals(hash2) ) {
     				maxSum += Math.max(count1, count2);
     				minSum += Math.min(count1, count2);
     				i++;
diff --git a/src/test/org/openscience/cdk/similarity/TanimotoTest.java b/src/test/org/openscience/cdk/similarity/TanimotoTest.java
index 3848087cdb0..267402736df 100644
--- a/src/test/org/openscience/cdk/similarity/TanimotoTest.java
+++ b/src/test/org/openscience/cdk/similarity/TanimotoTest.java
@@ -188,18 +188,26 @@ public void testRawTanimotoBetween0and1() throws Exception {
     }
     
     @Test
-    public void testCountMethod1and2() {
-		IntArrayCountFingerprint fp1 = new IntArrayCountFingerprint(
-                                           new HashMap<String, Integer>() {{
-             	                               put("A", 3);
-                                           }}
-            		                       );
-		IntArrayCountFingerprint fp2 = new IntArrayCountFingerprint(
-                                           new HashMap<String, Integer>() {{
-             	                               put("A", 4);
-                                           }}
-                                       );
+    public void testCountMethod1and2() throws CDKException {
+    		ICountFingerprint fp1 = new IntArrayCountFingerprint(
+                                    new HashMap<String, Integer>() {{
+             	                        put("A", 3);
+                                    }}
+            		                );
+    		ICountFingerprint fp2 = new IntArrayCountFingerprint(
+                                    new HashMap<String, Integer>() {{
+             	                        put("A", 4);
+                                    }}
+                                );
 		Assert.assertEquals(0.923, Tanimoto.method1(fp1, fp2), 0.001 );
 		Assert.assertEquals(0.75, Tanimoto.method2(fp1, fp2), 0.001 );
+		
+		Molecule mol1 = MoleculeFactory.makeIndole();
+        Molecule mol2 = MoleculeFactory.makeIndole();
+        SignatureFingerprinter fingerprinter = new SignatureFingerprinter();
+        fp1 = fingerprinter.getCountFingerprint(mol1);
+        fp2 = fingerprinter.getCountFingerprint(mol2);
+        Assert.assertEquals(1.0, Tanimoto.method1(fp1, fp2), 0.001);
+        Assert.assertEquals(1.0, Tanimoto.method2(fp1, fp2), 0.001);
     }
 }
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