We are operating two e-commerce stores - both selling the exact same products but with different currencies and target countries. We get more links pointing towards one site only. Which URL structure would be good to merge the 2 sites - through a sub directory like www.mysite.com/in or a sub-domain like http://in.mysite.com so that the SEO links benefit both the stores?
Well it depends on you, I would choose the second one (the sub-domain), as you can use the SAME URL structure for both versions. Example: If you have a TOP products section it would be better to look like this: mysite.com/top in.mysite.com/top Otherwise it would look like this: mysite.com/in/top → Which is a little bit strange.. But it depends on your decision!