Two domains One hosting account

[DavetheExterminator]

I have two separate domains set up on one hosting account through godaddy.  Will this affect the SEO negatively?  They are completely different sites with their own unique domains but on my local files the second domain is set up as a subfolder for the original hosted domain.  Any thoughts?  Thanks in advance.

[Malarowski]

SEO cares about domains, not what space they use. If they are set up as domain and sub-domain they won't be affecting each other.

[akaigotchi]

Mike said it all. What could affect your SEO in a way, although only very slightly: Reciprocal links from both domains to the other domain. As they both reside on the same webspace, which is obviously on the same server, that has the very same IP-adress for both servers... they both sit on the same Class-C IP-network. Links from domains that reside on the same Class-C tend to not have the same impact as links from other Class-C networks. But as your linkbuilding shouldn't rely too much on two links you won't run into massive trouble here.