Marine Mammal Cooperative Agreements in Alaska Amendments Act of 2008

Marine Mammal Cooperative Agreements in Alaska Amendments Act of 2008 - Amends the Marine Mammal Protection Act of 1972 to authorize the Secretary of the department in which the National Oceanic and Atmospheric Administration (NOAA) is operating to enter into cooperative agreements with Alaska Native organizations to conserve and manage (currently, to conserve) any stock of marine mammals. Sets forth allowed contents of agreements and required aspects of harvest management plans.

Makes it unlawful for any Alaska Native within the geographic area to which a harvest management plan applies to take, transport, sell, or possess a marine mammal in violation of the provisions of that plan.

Modifies the uses of related grants to Alaska Native organizations, including allowing: (1) monitoring marine mammal harvesting for subsistence and handicraft (currently, for subsistence) uses; and (2) participating in marine mammal research conducted by the state of Alaska (currently, by states).