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Is it supported to install a Certification Authority service on a Windows Server 2008 R2 joined on a 2003 native functional level domain?

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Yes.

However, to get the full functionality of the newer CA (particularly version 3 templates) you'll need to run the 2008 schema upgrades (I don't believe the R2 schema changes impact certificates at all) - which does not require a functional level change or even any newer domain controllers.

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