I can find my website in google only as "http://www.mysite.com/index.php" and not at all as "http://www.mysite.com" (even in searches).
Why is that? Can I fix it? Does it affect rankings?
Yes it can affect ranking because it splits link pop between domain and domain/index.xxx.
Make sure all your internal links to the home page are to "/" not "/index.php".
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A foolish consistency is the hobgoblin of little minds
Thought for today:- Is SEO the only industry where all the cowboys are Indians?
I can find my website in google only as "http://www.mysite.com/index.php" and not at all as "http://www.mysite.com" (even in searches).
Why is that? Can I fix it? Does it affect rankings?
Well, maybe and maybe not. It's hard to speak of a search without
knowing the domain name, could you tell us?