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I have currently two Unix-based DNS servers. What is the best method of migrating these to Windows 2003 DNS? Or can Windows 2003 domain work with these DNS servers?
A Windows 2003 domain can work with UNIX servers, although it is my experience that it doesn't work nearly as smoothly as using Windows DNS. The problem is Microsoft's use of non-standard non-RFC compliant characters. While a UNIX DNS server that allows SRV records and automatic updates is said to be acceptable, the use of the underscore character by the Active Directory services tends to cause some problems.
To convert a UNIX system to a Windows DNS is not too difficult. You set the Windows 2003 server DNS up as a secondary zone. Then you point to the UNIX DNS as the primary. You allow the Windows server to do a zone transfer. Now you have all of the DNS information on Windows. Convert the zone to primary. Then, dcpromo the machine to a domain controller. Finally convert the zone to an AD integrated zone. All of the DNS information that was on UNIX will still be there.