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I have a blog at domain.wordpress.com and I'm buying the custom domain domain.com.

Which domain (domain.wordpress.com or domain.com) should I register in Google Webmaster Tools?

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It depends on what you are going to do in the future.

If you are going to continue to host the site at wordpress.com and just activate their custom domain name service, then both domain.com and domain.wordpress.com will work and you can register either one.

If you plan on moving to self-hosted WordPress in the future or plan on doing something else with the domain that will eventually remove it from wordpress.com, then register domain.com at GWT.

Generally speaking, it is always better to register the domain name that is fully under your control (domain.com) than one under someone else's control.

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