Bottom Trawl and Deep Sea Coral Habitat Act

Bottom Trawl and Deep Sea Coral Habitat Act - Requires the Secretary of Commerce to direct the Under Secretary for Oceans and Atmosphere to explore, identify, research, and map the locations of deep sea corals and deep sea sponges.

Directs the Secretary to develop a cooperative research program to identify: (1) the ideal areas for the use of bottom trawls; and (2) the locations of deep sea corals and deep sea sponges.

Requires each Regional Fishery Management Council to submit to the Secretary a list of areas that were fished using bottom trawls during the seven-year period ending on December 31, 2004, including recommendations of which areas should be designated as Bottom Trawl Zones. Requires the Secretary to designate each area that does not contain a deep sea coral and sponge ecosystem as a Bottom Trawl Zone. Prohibits the use of bottom trawls in an area not designated as a Bottom Trawl Zone.

Directs the Secretary to designate as a Coral Habitat Conservation Zone each area that a Council has designated as an area in which the use of bottom trawls is prohibited for the protection of seafloor habitat, or for which a map and best available data has detected the presence of deep sea corals or deep sea sponges.

Sets forth both civil and criminal penalties for persons who violate the requirements under this Act.

Authorizes the President to permit the Secretary to work with appropriate international organizations and foreign nations to develop data to identify areas in international waters that contain deep sea corals or deep sea sponges and to protect such deep sea corals or deep sea sponges.