Yes, there is a new native layer called "Windows Phone Runtime", which is a partial, semi-overlapping subset of the Windows Runtime found in Windows 8.
However, it's partial and incomplete, and mostly targeted at game developers - to access most of the features of Windows Phone 8, you need to write your apps in a managed language, accessing the .NET API for Windows Phone, which is pretty much the same as it's always been, with a few minor incompatibilities, even in so-called "compatibility mode" for WP7 apps.
EDIT: That was a hideous run-on sentence, but I kinda like it.