Conservation planning in San Diego County has been ongoing since the early 1990’s and has resulted in the establishment of the Multiple Species Conservation Program (MSCP) in southwest San Diego County and the Multiple Habitat Conservation Program (MHCP) in northwest San Diego County. Currently, the County of San Diego is developing regional plans for the unincorporated lands remaining in north and east San Diego County. These regional plans are (or will be) permitted under the Federal Endangered Species Act (Section 10: Habitat Conservation Plan) and the State of California Natural Community Conservation Planning Act. This paper focuses on the integration of transportation conservation with the MSCP. “The MSCP is a comprehensive, long-term habitat conservation plan which addresses the needs of multiple species and the preservation of natural vegetation communities in San Diego County” (MSCP 1998). The MSCP covers 85 species, of which 20 species are federally listed and 14 are State listed, including 46 plant species and 39 animal species. The MSCP defines a design preserve within the plan boundaries that include large interconnected areas for the protection of the MSCP-covered species. The MSCP does not cover regional transportation projects, such as projects funded by the Federal Highway Administration. District 11 of the California Department of Transportation and the Federal Highway Administration collaborated with Federal and State resource agencies to develop transportation projects that are consistent with the MSCP. The planning and development of improvements to Interstate 15, State Route (SR) 125 South, and the SR 905 Extension included the protection of large blocks of habitat in conservation banks. Numerous parcels were purchased as mitigation, including the Walsh property, Bonita Meadows Open Space Preserve, Johnson Canyon Open Space Preserve, San Ysidro Mountain, Lake Jennings, and Dennery Canyon. These parcels are key to the buildout of the preserve identified by MSCP. In addition, the design of SR 125 South and the SR 905 Extension included modifying the alignment to avoid and minimize impacts to sensitive natural resources within the MSCP. Collaboration between the transportation agencies and natural-resource agencies has resulted in the preservation of large blocks of habitat to further the buildout of the MSCP preserve. The voter-approved extension of a $0.005 sales tax will provide a funding mechanism for the up-front purchases of land to continue this collaboration in recognition that it results in the most cost-effective mitigation and better conservation.