diff --git a/src/calibre/ebooks/epub/output.py b/src/calibre/ebooks/epub/output.py
index 4bc0f679cc..2e254e99cc 100644
--- a/src/calibre/ebooks/epub/output.py
+++ b/src/calibre/ebooks/epub/output.py
@@ -101,6 +101,13 @@ class EPUBOutput(OutputFormatPlugin):
             )
         ),
 
+        OptionRecommendation(name='epub_flatten', recommended_value=False,
+            help=_('This option is needed only if you intend to use the EPUB'
+                ' with FBReaderJ. It will flatten the file system inside the'
+                ' EPUB, putting all files into the top level.')
+        ),
+
+
         ])
 
     recommendations = set([('pretty_print', True, OptionRecommendation.HIGH)])
@@ -142,8 +149,12 @@ class EPUBOutput(OutputFormatPlugin):
     def convert(self, oeb, output_path, input_plugin, opts, log):
         self.log, self.opts, self.oeb = log, opts, oeb
 
-        from calibre.ebooks.oeb.transforms.filenames import UniqueFilenames
-        UniqueFilenames()(oeb, opts)
+        if self.opts.epub_flatten:
+            from calibre.ebooks.oeb.transforms.filenames import FlatFilenames
+            FlatFilenames()(oeb, opts)
+        else:
+            from calibre.ebooks.oeb.transforms.filenames import UniqueFilenames
+            UniqueFilenames()(oeb, opts)
 
         self.workaround_ade_quirks()
         self.workaround_webkit_quirks()
diff --git a/src/calibre/gui2/convert/epub_output.py b/src/calibre/gui2/convert/epub_output.py
index c1ef6282f7..2fcbd751fe 100644
--- a/src/calibre/gui2/convert/epub_output.py
+++ b/src/calibre/gui2/convert/epub_output.py
@@ -21,7 +21,7 @@ class PluginWidget(Widget, Ui_Form):
         Widget.__init__(self, parent,
                 ['dont_split_on_page_breaks', 'flow_size',
                     'no_default_epub_cover', 'no_svg_cover',
-                    'preserve_cover_aspect_ratio',]
+                    'preserve_cover_aspect_ratio', 'epub_flatten']
                 )
         for i in range(2):
             self.opt_no_svg_cover.toggle()
diff --git a/src/calibre/gui2/convert/epub_output.ui b/src/calibre/gui2/convert/epub_output.ui
index abca2405e8..a0d9570226 100644
--- a/src/calibre/gui2/convert/epub_output.ui
+++ b/src/calibre/gui2/convert/epub_output.ui
@@ -81,6 +81,13 @@
      </property>
     </spacer>
    </item>
+   <item row="1" column="1">
+    <widget class="QCheckBox" name="opt_epub_flatten">
+     <property name="text">
+      <string>&amp;Flatten EPUB file structure</string>
+     </property>
+    </widget>
+   </item>
   </layout>
  </widget>
  <resources/>
diff --git a/src/calibre/gui2/tools.py b/src/calibre/gui2/tools.py
index fc84e88d09..d18cc61baf 100644
--- a/src/calibre/gui2/tools.py
+++ b/src/calibre/gui2/tools.py
@@ -236,6 +236,10 @@ def fetch_scheduled_recipe(arg):
         recs.append(('header', True, OptionRecommendation.HIGH))
         recs.append(('header_format', '%t', OptionRecommendation.HIGH))
 
+    epub = load_defaults('epub_output')
+    if epub.get('epub_flatten', False):
+        recs.append(('epub_flatten', True, OptionRecommendation.HIGH))
+
     args = [arg['recipe'], pt.name, recs]
     if arg['username'] is not None:
         recs.append(('username', arg['username'], OptionRecommendation.HIGH))