Magnuson-Stevens Act Amendments of 2000 - Title I: Fishery Management and Enforcement - Amends the Magnuson-Stevens Fishery Conservation and Management Act to: (1) include Caribbean Sea commonwealths, territories, and possessions of the United States within the area of the Caribbean Fishery Management Council; (2) outline procedures for fishery management council appointments; (3) require fishery management plans to give priority to habitat areas of particular concern; (4) allow such plans to designate and protect zones encompassing coral reef and other sensitive habitats; (5) require the appropriate fishery council and Secretary of Commerce to ensure that any exclusive quota-based fishery program meets specified requirements; (6) require each council to establish a committee to recommend changes to quota-based programs; (7) require the Secretary to evaluate each plan or plan amendment for consistency with national standards; (8) direct the Secretary to establish guidelines for describing and identifying essential fish habitat and areas of particular concern for a fishery; and (9) provide for marine law enforcement cooperative agreements.

Directs the Secretary to report on the implementation of fish bycatch requirements. Authorizes a system of incentives to reduce bycatch and bycatch rates in fisheries.

Requires each council to submit a fishery ecosystem management plan.

Requires the National Academy of Sciences to recommend improvements for the Federal fishery management process.

Title II: Fisheries Data Collection, Research, and Assessment - Requires: (1) a regional fisheries outreach program; (2) an independent peer review of fishery management methods; (3) a National Observer Program; and (4) a national cooperative research and management program.

Authorizes the Secretary to acquire up to six fishery survey vessels.

Title III: Capacity Reduction - Directs the National Marine Fisheries Service to evaluate and identify the overcapacity in each fishery designated as overfished or approaching such condition.

Title IV: Reauthorization - Extends through FY 2005 the authorization of appropriations for the Act.