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If I have two active directory domains that have the same netbios domain name, but different fully qualified domain names, can they trust each other (one-way, two-way, etc.)?

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No this is 100% not supported or working. I have this exact scenario in my environment. Your options are domain rename or creating child domains that have trusts between each other and using resources between the child domains via a two way trust.

Another option is new domain and migrate, which might sound difficult but if it's a small amount of objects it can be done in a few hours with little downtime.

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Thanks for the response! – Kirk Liemohn Feb 11 '11 at 14:45
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Pretty sure it's not supported scenario by Microsoft. However, you might be able to configure it if you going to use DNS name only while building cross-domain communication. I would highly suggest checking into domain rename scenario. However if you have Exchange in the domain - reinstall. Renaming a domain with Exchange in it is a prescription for permanent headache.

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Thanks for the quick response. – Kirk Liemohn Feb 11 '11 at 14:46
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To add to my previous comment, if you'll be able to separate the LAN where domains are located, e.g. different subnets, the chance of this to work will be higher, the reason to this is that starting Windows 2000 Microsoft getting away from using NETBIOS as the main resolution mechanism. The way resolution worked BEFORE Windows 2000 was - WINS, lmhosts file, DNS, hosts file. Since Windows 2000 the order is reverted - DNS, hosts file, WINS, lmhosts file. – Vick Vega Feb 11 '11 at 14:53

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