When I installed Exchange 2003 for a customer several years ago, their Active Directory was as simple as can be. One Forest, One site and One exchange Organization. A few years later, they decided to add one domain for business reasons and users in this new business unit were move to the new domain and assigned to new specific Exchange OWA servers but the split never went further, so they still have one forest, two domains and only one Exchange Organization.

Migration to Exchange 2010 seemed like an easy project: Install two dags (one per domain), and the clients would be automatically redirected to the correct one based on their domain membership… or would they ?

In fact, NO.

Autodiscovery is being used by Outlook when you first open it (and it gets refreshed regularly), and is based on AD Site, not AD Domain. What it means is that outlook will try to find the Autodiscovery entry in AD, but only One entry will exist for a single AD site. If you want to split your exchange infrastructure based on domains, you will need to associate those domains with different sites.

What you need to do:

1. Link the Default-First-Site-Name to a valid Subnet that contains your Active Directory Domain Controllers and Exchange servers for the main user population

2. Create a new AD site that will contain the DCs and Exchange Servers for the second domain.

3. Make sure the Domain controllers for the new domain are part of the new site (this means the IPs must be part of the new site – this might lead you to add new DCs in the site by reinstalling them or changing their IP or using specific subnets that would allow you to split the same domain in two sites).

4. Only once your domain controllers are in place, you will be able to install Exchange servers in the new site.
Note that you don’t need to assign clients to the specific sites if you don’t want to (but this might be advised for other reasongs). Autodiscovery will work as soon as the Exchange servers are installed in their specific site.

There is a potential workaround involving the use of Xml files locally on the client to replace autodiscovery. After requesting the help of Microsoft Support on our problem, we were told that the use of local Xml files is not supported.

One last note is that Autodiscovery will try to update its settings regularly. If some of the settings are not correct (if you are testing Outlook Anywhere and set incorrect entries just to test) you might get prompts for the user to type in their password during normal Outlook usage. This type of problem is usually very difficult to trace back to this, so make sure your settings are ok.