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Web hosting providers offer services such as hosting multiple domains in one account. Then my concern is about seo friendliness. say the main domain of my account is maindomain.com on which I have added an addon domain say domain2.com. That means cpanel will generate domain2.maindomain.com and the contents of domain2.com will be practically stored into a subfolder in maindomain.com.

Now, assume both maindomain.com and domain2.com have same structure both optimized for seo same way. My question is that would maindomain.com links be more seo friendly due to that fact that maindomain.com is the mani domain of my account?

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up vote 3 down vote accepted

Search engines will have no idea which of the two domains is your 'main' domain. They have no access to your hosting providers data. They only know your domains from what they contain and how other sites link to them.

So, no, this will not affect SEO.

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The only thing I would add is that domain2.maindomain.com (the subdomain) should redirect to domain2.com to avoid the possibility of any duplicate content issues. –  w3d Aug 27 '12 at 14:21
    
Sure domain2.maindomain.com redirects to domain2.com by default in cpanel. However, I remove domain2.maindomain.com as I want my visitors to get to my website only via domain2.com and I dont want google lists any domain2.maindomain.com urls. –  C graphics Aug 27 '12 at 19:52
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