The present invention includes systems for and methods of visually integrating application windows in a virtual machine environment. Embodiments of the present invention are directed to a system for and method of visually integrating application windows of host and guest operating system in a virtual machine environment in order to reduce difficulties that the users of computers experience in navigating between applications in a virtual machine environment. The present invention accomplishes this by using a composite window list in the virtual machine monitor (VMM) to manage the configuration, the focus, the geometry, the Z-order of the windows across guest and host operating systems, and the arrangement of doppelgangers (virtual application windows, in this case) in a way that allows host and guest application windows to appear integrated in a single display window.