Microsite as a stand-alone site under one domain and sub-domained under another: duplicate content penalty?

[marketing-iq]

We developed and maintain a microsite (example: www.coolprograms.org) for a non-profit that lives outside their main domain name (www.nonprofit-mainsite.org) and features content related to a particular offering of theirs.

They are utilizing a Google Grant to run AdWords campaigns related to awareness.  They currently drive traffic from the AdWords campaigns to both the microsite (www.coolprograms.org) and their main site (www.nonprofit-mainsite.org).  Google recently announced a change in their policy regarding what domains a Google Grant recipient can send traffic to via AdWords: https://support.google.com/nonprofits/answer/1657899?hl=en.  The ads must all resolve to one root domain name (nonprofit-mainsite.org).

If we were to subdomain the microsite (example: coolprograms.nonprofit-mainsite.org) and keep serving the same content via the microsite domain (www.coolprograms.org) is there a risk of being penalized for duplicate content?

Are there other things we should be considering?

[Graphics_Online_SEO]

You can use the 'rel = "canonical" tag' on your microsite to specify that "coolprograms.nonprofit-mainsite.org" is the preferred domain for indexing.

http://support.google.com/webmasters/bin/answer.py?hl=en&answer=139394

[marketing-iq]

Thanks Graphics Online! That's what we were thinking.  Good to have an opinion posted back.  I'll try to post back and let you know how it goes after implementation.