A command decoder used for a microcontroller based Flash memory digital controller system includes multiple subsystems, including the command decoder, which serves as the main user interface for interpreting commands from a user and managing the priority of commands and command modes. The command decoder also stores crucial information including address, data, opcodes, and various flags registers that are used by other subsystems including the program buffer, burst read module, register block, and microcontroller. In addition, the command decoder contains clock synchronization logic, controls the sleep function of the microcontroller and serves as a test mode controller.