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The README should be enough to put you in the right direction. The one weird thing I had to do to get my stylesheet on the server is to manually parse webpack stats:

const chunks = JSON.parse(fs.readFileSync('./dist/assets/webpack-chunks.json', 'utf8'))
const style = chunks['styles']['main']

// And then where I'm rendering my server markup:
{style && <link rel='stylesheet' href={style} />}

I'm also using webpack v1 so things have probably changed quite a lot. I recommend you try to find a good boilerplate or tutorial to follow that handles server-side rendering with CSS Modules.

There's also isomorphic-style-loader that supposedly allows your CSS to work both client and server side, and they even have a CSS Modules example. I don't remember exactly why I didn't use it (probably because I didn't like using the withStyles HoC), but if it's easier to setup I recommend giving that a shot.