Qubes is an operating system primarily running on hardware, based on Xen, security by compartmentalization, with templates for VMs available for Fedora, Debian, and Qubes-Whonix.
Whonix is an operating system primarily running inside VMs. Supported platforms include VirtualBox, KVM and Qubes.
Qubes and Whonix do cooperate. Whonix is easy available and well supported in Qubes, called Qubes-Whonix.