The concept of a "subsystem" in Windows has evolved since the operating system's inception when Windows NT was designed to support multiple operating system environments through distinct subsystems. Win32 subsystem, which features case-insensitive filenames and device files in every directory, and the POSIX subsystem, which supports case-sensitive filenames and centralized device files: Windows subsystem, the Subsystem for Unix-based Applications (SUA), and the Native subsystem for kernel-mode code were the main subsystems at first.

/SUBSYSTEM linker switch was used to specify the target subsystem at compile time, enabling applications to be compiled for different environments such as console applications, EFI boot environments, or native system processes.

In this nomenclature, WSL follows the original naming conventions (although SUA should have been called WSUA).