ArcGIS token is an efficient authentication method; it comes built in with Server and provides you with basic security. However, it might not be the most effective security mechanism. In some instances, you will have security in place, you will have roles and users set up on an LDAP or Windows domain, and it will become hectic to repopulate those into ArcGIS for Server. That is why Server provides a channel to connect your Server site to the Windows domain where you can inherit all the configurations and let the Web server do the authentication every time someone requests a secured resource.
To configure Web server security instead of tokens, access ArcGIS for Server Manager, click on Security, and edit Configuration Settings by clicking on the edit button. Choose the second option, Users and roles from an existing enterprise system (LDAP or Windows Domain), and then click on Next.
Server gives you the option to use an existing Windows domain...