Atlantic Highly Migratory Species Conservation Act of 2000

Atlantic Highly Migratory Species Conservation Act of 2000 - Prohibits any person from engaging in pelagic longline fishing in the: (1) Atlantic Conservation Zone for Highly Migratory Species (HMS); (2) Gulf of Mexico Conservation Zone for Swordfish from January 1 through Memorial Day; (3) Gulf of Mexico Conservation Zone for HMS from Memorial Day through Labor Day for the next four years; and (4) Mid-Atlantic Bight Conservation Zone from June 1 through September 30.

Directs the Secretary to conduct a voluntary Pelagic Longline Vessel Permit Holder Compensation Program, under which certain eligible permit holders are compensated for fish catch losses due to the prohibitions contained above.

Requires the revocation of all commercial fishing permits and licenses held by those accepting payments under this Act. Prohibits such vessels from fishing commercially anywhere in the world. Provides criminal and civil penalties for violations.

Prohibits those compensated from reentering the Directed Swordfish Limited Access Fishery or Atlantic Tuna Longline Fishery.

Establishes a fishery conservation fee system for repayment of direct loans made under this Act.

Considers a person violating this Act to have committed an act prohibited under the Magnuson-Stevens Fishery Conservation and Management Act.

Establishes within the National Marine Fisheries Service a Pelagic Longline Highly Migratory Species Bycatch and Mortality Reduction Research Program.

Directs the Secretary to: (1) reallocate to the U.S. commercial swordfish hand gear fishing fleet the total allowable catch from permit holders compensated under this Act; and (2) monitor effectiveness of fish area closures and minimize bycatch to conform to fishery limits.