Dirca occidentalis occurs in patchy populations within three separate areas near San Francisco. We used principle coordinate, cladistic, and molecular variance analyses of intersimple sequence repeats (ISSR) in DNA of 178 plants to demonstrate genetic separation of populations in the East Bay (Contra Costa and Alameda Counties), the North Bay (Marin and Sonoma Counties), and the Peninsula (San Mateo and Santa Clara Counties). We then assessed factors that may explain this genetic structure. Dirca occidentalis was found capable of reproducing both asexually and sexually, including via self-pollination. While the regulation and frequency of asexual spread remain uncertain, temperature and insolation were associated with large differences we observed in seed formation among individuals. Plants that bloomed relatively late during the winter of 2004-2005 in and near Jasper Ridge Biological Preserve on the Peninsula formed seeds at comparatively high rates. Among those plants, photosynthetic rates and seed formation increased linearly as midday insolation increased, suggesting seed set is influenced by plant carbon economy and/or activity of certain potential pollinators. Date of incipient flowering differed by over two months during the winter of 2006-2007 among 56 plants in various habitats, leading to variation in the extent to which low temperature may have reduced seed set through direct injury or via suppression of pollinators. Asexual recruitment, self-pollination, low rates of seed formation on many individuals, and the lack of long-distance pollen and seed dispersal appear to explain the strong correlation of genetic and geographic distance throughout the distribution of Dirca occidentalis.