I made a dark monokai syntax theme for Atom.

Originally converted from monokai which in turn came from the TextMate theme using the TextMate bundle converter.

atom monokai dark screenshot

I would also suggest editing your main stylesheet and adding the following CSS:

/* really nice smooth fonts */
body {
  -webkit-font-smoothing: antialiased;
  text-rendering: optimizeLegibility;
  -moz-osx-font-smoothing: grayscale;
}

/* custom scrollbars */
.tree-view-resizer {
  ::-webkit-scrollbar {
    width: 0.5em;
    height: 0.5em;
  }

  ::-webkit-scrollbar-track {
    background-color: #303030;
  }

  ::-webkit-scrollbar-thumb {
    background-color: lighten(#303030, 15%);
  }
}

/* fix website scroll styling flash */
.tree-view-scroller {
  overflow: hidden;
  &:hover {
    overflow: auto;
  }
}

This adds some nicer smoothing and also adds some custom scrollbars to both panes. This gets rid of the ugly strange white ones. I would also suggest checking out Source Code Pro for your font!

You can download the theme on Atom.