Atlantic Highly Migratory Species Conservation Act of 2001

Establishes under the National Marine Fisheries Service a pelagic longline fishing vessel capacity reduction program.

Directs the Secretary to conduct a voluntary Pelagic Longline Vessel Permit Holder Compensation Program, under which vessels prohibited from engaging in such commercial fishing are compensated for fish catch losses.

Requires the revocation of all commercial fishing permits or licenses held by those accepting payments under this Act, prohibiting such vessels from being used anywhere in the world for commercial fishing. Permits the transfer of a permit if the Secretary determines that the permit will not be used for pelagic longline fishing. Sets forth penalties for violators.

Establishes within the National Marine Fisheries Service at the Southeast Fisheries Science Center a Pelagic Longline Billfish Bycatch and Mortality Reduction Research Program to identify and test a variety of fishing gear configurations and uses for reducing highly migratory species mortality and sea turtle mortality in the exclusive economic zone of the United States in the Atlantic Ocean.

Provides for the reallocation to the United States commercial swordfish hand gear fishing fleet the portion of total allowable catch of swordfish by the United States pelagic longline fishing fleet that was attributable to vessels that were authorized to engage in fishing under revoked permits and licenses.

Prohibits any pelagic longline vessel from operating within the Atlantic Ocean highly migratory species fishery without an approved vessel monitoring device.