Yes, there are two distinct GACs as from .NET 4.0
See here: .NET 4.0 has a new GAC, why?
As stated below, the new physical location is %windir%\Microsoft.NET\assembly\ (you can interogate it using the dir command at a command prompt if you’re interested).
It’s worth noting that applications running up to the 2.0 CLR will not even be able to see assemblies in the new GAC.