diff --git a/src/coverlet.core/CoverageResult.cs b/src/coverlet.core/CoverageResult.cs
index b7caf6f5e..2c8d60789 100644
--- a/src/coverlet.core/CoverageResult.cs
+++ b/src/coverlet.core/CoverageResult.cs
@@ -44,7 +44,7 @@ internal void Merge(Modules modules)
         {
             foreach (var module in modules)
             {
-                if (!this.Modules.ContainsKey(module.Key))
+                if (!this.Modules.Keys.Select(Path.GetFileName).Contains(Path.GetFileName(module.Key)))
                 {
                     this.Modules.Add(module.Key, module.Value);
                 }