diff --git a/src/main/java/net/md_5/specialsource/JarMapping.java b/src/main/java/net/md_5/specialsource/JarMapping.java
index c7bdac3..bf6d71b 100644
--- a/src/main/java/net/md_5/specialsource/JarMapping.java
+++ b/src/main/java/net/md_5/specialsource/JarMapping.java
@@ -72,8 +72,8 @@ public class JarMapping {
     }
 
     /**
-     * Add a class name prefix to the mapping ignore list.
-     * Note: this only applies before loading mappings, not after
+     * Add a class name prefix to the mapping ignore list. Note: this only
+     * applies before loading mappings, not after
      */
     public void addExcludedPackage(String packageName) {
         SpecialSource.log("Protecting Package: " + packageName);
@@ -256,7 +256,11 @@ public class JarMapping {
 
         String line;
         while ((line = reader.readLine()) != null) {
-            if (line.startsWith("#") || line.isEmpty()) {
+            int commentIndex = line.indexOf('#');
+            if (commentIndex != -1) {
+                line = line.substring(0, commentIndex);
+            }
+            if (line.isEmpty()) {
                 continue;
             }
 
@@ -369,8 +373,8 @@ public class JarMapping {
             }
 
             if (packages.containsKey(oldPackageName) && !newPackageName.equals(packages.get(oldPackageName))) {
-                throw new IllegalArgumentException("Duplicate package mapping: " + oldPackageName + " ->" + newPackageName +
-                " but already mapped to "+packages.get(oldPackageName)+" in line="+line);
+                throw new IllegalArgumentException("Duplicate package mapping: " + oldPackageName + " ->" + newPackageName
+                        + " but already mapped to " + packages.get(oldPackageName) + " in line=" + line);
             }
 
             packages.put(oldPackageName, newPackageName);
@@ -400,7 +404,7 @@ public class JarMapping {
             }
 
             if (isExcludedPackage(oldClassName)) {
-                SpecialSource.log("Ignored FD: " + oldClassName + "/" + oldFieldName + " -> " +  newFieldName);
+                SpecialSource.log("Ignored FD: " + oldClassName + "/" + oldFieldName + " -> " + newFieldName);
                 return;
             }
 
@@ -435,7 +439,7 @@ public class JarMapping {
             }
 
             if (isExcludedPackage(oldClassName)) {
-                SpecialSource.log("Ignored MD: " + oldClassName + "/" + oldMethodName + " -> " +  newMethodName);
+                SpecialSource.log("Ignored MD: " + oldClassName + "/" + oldMethodName + " -> " + newMethodName);
                 return;
             }