A cap system for subsea equipment that can be employed on various subsea equipment including but not limited to a vertical monobore tree, a horizontal tree, a wellhead and a tubing head spool. The cap system includes a cap assembly that has the flexibility of installation and retrieval for open water as well as a through a riser with a running tool. The cap assembly also does not require any orientation during installation. The cap system includes a debris cap assembly installable in engagement with the cap assembly. The debris cap assembly interfacing with the cap assembly provides the ability to inject and bleed fluids through a main bore and an annulus bore of the subsea tree independently and without removal of the debris cap assembly and cap assembly.