diff --git a/DATabase/MergeDiff.cs b/DATabase/MergeDiff.cs
index e087da81..57ce3eba 100644
--- a/DATabase/MergeDiff.cs
+++ b/DATabase/MergeDiff.cs
@@ -100,23 +100,40 @@ namespace SabreTools
 			}
 
 			// Create a dictionary of all ROMs from the input DATs
+			int i = 0;
 			Dictionary<string, List<RomData>> dict = new Dictionary<string, List<RomData>>();
 			foreach (string input in _inputs)
 			{
 				_logger.User("Adding DAT: " + input);
-				dict = RomManipulation.ParseDict(input, 0, 0, dict, _logger);
+				dict = RomManipulation.ParseDict(input, i, 0, dict, _logger);
+				i++;
 			}
 			
 			// Modify the Dictionary if necessary and output the results
 			if (_diff || _ad)
 			{
-				// Get all entries that have only one item in their list
+				// Get all entries that don't have External dupes
 				Dictionary<string, List<RomData>> diffed = new Dictionary<string, List<RomData>>();
 				foreach (string key in dict.Keys)
 				{
-					if (dict[key].Count == 1)
+					List<RomData> temp = dict[key];
+					temp = RomManipulation.Merge(temp);
+
+					foreach (RomData rom in temp)
 					{
-						diffed.Add(key, dict[key]);
+						if ((_dedup && rom.Dupe != DupeType.InternalHash) || (!_dedup && rom.Dupe != DupeType.InternalAll))
+						{
+							if (diffed.ContainsKey(key))
+							{
+								diffed[key].Add(rom);
+							}
+							else
+							{
+								List<RomData> tl = new List<RomData>();
+								tl.Add(rom);
+								diffed.Add(key, tl);
+							}
+						}
 					}
 				}
 
diff --git a/SabreHelper/Enums.cs b/SabreHelper/Enums.cs
index d3520de4..e2345949 100644
--- a/SabreHelper/Enums.cs
+++ b/SabreHelper/Enums.cs
@@ -50,4 +50,16 @@ namespace SabreTools.Helper
 		WARNING,
 		ERROR,
 	}
+
+	/// <summary>
+	/// Determines which type of duplicate a file is
+	/// </summary>
+	public enum DupeType
+	{
+		None = 0,
+		InternalHash,
+		ExternalHash,
+		InternalAll,
+		ExternalAll,
+	}
 }
diff --git a/SabreHelper/RomManipulation.cs b/SabreHelper/RomManipulation.cs
index 142ed412..58b4affc 100644
--- a/SabreHelper/RomManipulation.cs
+++ b/SabreHelper/RomManipulation.cs
@@ -628,7 +628,30 @@ namespace SabreTools.Helper
 						last.CRC = (last.CRC == "" && rom.CRC != "" ? rom.CRC : last.CRC);
 						last.MD5 = (last.MD5 == "" && rom.MD5 != "" ? rom.MD5 : last.MD5);
 						last.SHA1 = (last.SHA1 == "" && rom.SHA1 != "" ? rom.SHA1 : last.SHA1);
-						last.Dupe = true;
+
+						// If the duplicate is in the same system and dupe is not already set to External
+						if ((last.SystemID == rom.SystemID || last.SourceID == rom.SourceID) && last.Dupe != DupeType.ExternalHash)
+						{
+							if (last.Game == rom.Game && last.Name == rom.Name)
+							{
+								last.Dupe = DupeType.InternalAll;
+							}
+							else
+							{
+								last.Dupe = DupeType.InternalHash;
+							}
+						}
+						else
+						{
+							if (last.Game == rom.Game && last.Name == rom.Name)
+							{
+								last.Dupe = DupeType.ExternalAll;
+							}
+							else
+							{
+								last.Dupe = DupeType.ExternalHash;
+							}
+						}
 
 						outroms.RemoveAt(outroms.Count - 1);
 						outroms.Insert(outroms.Count, last);
diff --git a/SabreHelper/Structs.cs b/SabreHelper/Structs.cs
index 7e2647bf..e77a77f1 100644
--- a/SabreHelper/Structs.cs
+++ b/SabreHelper/Structs.cs
@@ -18,6 +18,6 @@
 		public string CRC;
 		public string MD5;
 		public string SHA1;
-		public bool Dupe;
+		public DupeType Dupe;
 	}
 }