From the FAQ page regarding the marine license:

If I enroll in the federal registry can I fish in CT or any other state’s waters where a state license is required?
No. A state issued marine fishing license would still be required in CT and in other states having their own license.

What is the federal registry?
Effective January 1, 2010, federal law requires marine anglers to register with the National Saltwater Angler Registry Program unless the angler is exempted by having a marine waters fishing license issued by a state with a qualified licensing program. Connecticut’s MWFL is designed to satisfy the requirements for an exemption from the federal registry. The registry requirement is part of a major effort to improve the quality of recreational fishery statistics used in fisheries management. For more information on the federal registry visit: http://www.countmyfish.noaa.gov