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My website is physically located at example.com/websitedirectory.

I am masking the folder so that the document root folder is redirected to /websitedirectory and the folder is masked, so that it displays as example.com from the outside.

Does this have any impact on SEO?

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I am going to assume you mean that any request for example.com/page.html outputs the content of the file from websitedirectory/page.html. If it was "redirected" then the browser would show the subfolder in the URL.

In your case, there is no effect on SEO. Search engines will see the same URLs you see in your browser and won't know about the subdirectory unless you link directly to it.

One tiny thing to note: with your system it's likely that requesting the subdirectory page also works. In other words, loading example.com/websitedirectory/page.html gives the same content as example.com/page.html. This isn't an issue if no one knows about the subfolder (i.e. you don't link to it anywhere), but if the issue comes up it can be solved by using rel=canonical.

Incidentally, your site would be "physically" located at something like /var/www/example.com/websitedirectory on the server. Your host probably has it set so your domain points to the folder /var/www/example.com

If you have full server access then you should set up the "virtual host" to point to the subfolder, as that makes things simpler for yourself (but still makes no difference for SEO).

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I don't have root access so I can't change the physical access. I expected it not having an effect (as I am using it on multiple sites and haven't noticed any issues) but wanted to know if I might have missed something. Will keep this question opened for a few more days to see if there is anything that I have missed. –  Marek Andreansky Apr 11 at 12:33
    
I did forget to mention one tiny thing in my answer, which I have now added. But again, shouldn't make a difference. –  DisgruntledGoat Apr 11 at 17:16

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