Thanks for your reply.

An article I read recently suggested that using nofollow on links on the same website may not be a good idea as "if the website doesn't trust its own pages by having a nofollow, then why would Google want to put trust in it." Does this make sense? Would a subdomain be considered as a completely different site?

My other concern is using nofollow extensively may raise a flag to Google as a site that is heavily seo optimized or tries to manipulate its linking strategy.

Any more thoughts? The website is done 100% for users. All I am looking for is the best practice to follow to maximize the seo efforts in this area.

Hi,

I run a hotel booking site and the booking engine is setup on a subdomain.
 The subdomain is disabled from being indexed in robots.txt

Should the links from the main domain have a nofollow to the subdomain? What are you thoughts?

Thanks!