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I have a new wordpress multisite setup.

The main language is Italian and there are two subdomains using en and de for english and german.

There is no auto translation plugins being used.

The wordpress theme being used is by Studiopress.com and have SEO built in.

I am a little confused as which domains to use in Webmasters Tools.

If I use the subdomains (en and de) which have the seo setup, then google will index and show the en.example.it It won't know about the mapped domains or display them.

If I use the mapped domains then won't google not see the seo for the subdomains.

I am muddled about this.

What should I do?

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You should use Google's new markup for multi-lingual content:

<link rel="alternate" hreflang="it" href="http://www.example.com/" />
<link rel="alternate" hreflang="de" href="http://de.example.com/" />
<link rel="alternate" hreflang="en" href="http://en.example.com/" />
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