This document is Phase II of a biogeographic assessment completed in 2004, described below. In the spring of 2001, NOAA’s National Marine Sanctuary Program (NMSP) and National Centers for Coastal Ocean Science (NCCOS) launched a project to assess biogeographic patterns of selected marine species and habitats found within and adjacent to the boundaries of three west coast National Marine Sanctuaries off north/central California: Monterey Bay, Gulf of the Farallones and Cordell Bank. Sanctuary staff were conducting a joint review to update sanctuary management plans. To support this review, the NCCOS’s Biogeography Branch led a partnership effort to conduct a robust analytical assessment to define important biological areas and time periods within and adjacent to current sanctuary boundaries. The assessment was based on a synthesis of many data sets that were provided by project partners. Phase I assessment products include a CD-ROM and website containing two reports, geographic analyses and related data and results, hundreds of maps, a description of the ecosystem components and their linkages, and future activities to be addressed in Phase II. Phase II was initiated in the autumn of 2004 to complete the analyses of marine mammals and to update the marine bird colony information. In addition to updates to the bird and mammal chapters, an environmental settings chapter was added, containing new data and maps as well as existing maps and information from related NCCOS reports on the region. Results of these assessments are being used to assist the NMSP and state of California in addressing issues such as: evaluating potential modification of sanctuary and reserve boundaries, and changing management strategies or administration based on the principles of biogeography.