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Assuming that you have no options (and I really hate to see anyone rely on iFrames in 2012, especially for the home-page - it's a recipe for problems), I agree with Sanket - you can put a rel-canonical tag on the sub-domain pointing back to the main URL. That should at least help Google consolidate the pages. Unfortunately, it's very likely you're losing ranking value for the content in that frame. There are ways to host content on sub-domains, but mask/rewrite the URLs so that they look like they're part of the main domain. Load-balancing systems (with content across multiple IPs and sub-domains) do it all the time. Obviously, I don't know the details of your situation, but I'd strongly recommend looking for a more permanent solution. The canonical tag will be a bandage here, at best.