diff --git a/packages/babel-cli/bin/babel/dir.js b/packages/babel-cli/bin/babel/dir.js
index 6c7b2f41cc..43c401046d 100644
--- a/packages/babel-cli/bin/babel/dir.js
+++ b/packages/babel-cli/bin/babel/dir.js
@@ -14,7 +14,8 @@ module.exports = function (commander, filenames, opts) {
     var dest = path.join(commander.outDir, relative);
 
     var data = util.compile(src, {
-      sourceFileName: slash(path.relative(dest + "/..", src))
+      sourceFileName: slash(path.relative(dest + "/..", src)),
+      sourceMapName: path.basename(relative)
     });
     if (data.ignored) return;
 
diff --git a/packages/babel-cli/bin/babel/file.js b/packages/babel-cli/bin/babel/file.js
index 7830fb67b4..b03553a8ce 100644
--- a/packages/babel-cli/bin/babel/file.js
+++ b/packages/babel-cli/bin/babel/file.js
@@ -16,7 +16,8 @@ module.exports = function (commander, filenames, opts) {
 
   var buildResult = function () {
     var map = new sourceMap.SourceMapGenerator({
-      file: slash(commander.outFile || "stdout")
+      file: path.basename(commander.outFile) || "stdout",
+      sourceRoot: opts.sourceRoot
     });
 
     var code = "";