Windows Server 2008 DNS Server and Root Hints Location

Solution 1:

They can be loaded from the cache.dns server, but they also can be loaded from active directory.

If your DNS server is also a DC, it will automatically load root hints from AD first. If it is not a DC, it will use the cache.dns file.

Any customization of the Root Hints are stored at:

DC=RootDNSServers,CN=MicrosoftDNS,DC=DomainDnsZones,DC=<company>,DC=<tld>

As Shane mentioned, I believe the copy in the Domain partition is used for backwards compatibility.