Here we report on vertebrate fossil assemblages from two late Quaternary localities in the eastern San Francisco Bay region, Pacheco 1 and Pacheco 2. At least six species of extinct mammalian megaherbivores are known from Pacheco 1. The probable occurrence of Megalonyx jeffersonii suggests a late Pleistocene age for the assemblage. Pacheco 2 has yielded a minimum of 20 species of mammals, and provides the first unambiguous Quaternary fossil record of Urocyon, Procyon, Antrozous, Eptesicus, Lasiurus, Sorex ornatus, Tamias, and Microtus longicaudus from the San Francisco Bay region. While a radiocarbon date of 405 ± 45 RCYBP has been obtained for a single bone sample from Pacheco 2, the possibility that much of the assemblage is considerably older than this date is suggested by (1) the substantial loss of collagen in all other samples for which radiocarbon dating was unsuccessfully attempted and (2) the occurrence of Microtus longicaudus approximately 160 km to the west of, and 600 m lower in elevation than, its present range limit. The taphonomic data and limited stratigraphic information for the two localities suggest deposition of bones within a riparian system. Multiple lines of evidence including the taxonomic composition and the relative abundance of skeletal elements point to the original accumulation of most, if not all, of the small vertebrate remains at Pacheco 2 by owls. Based on taxonomic composition, Pacheco 1 appears to have been located in a mosaic of grassland and woodland habitats, and Pacheco 2 in moist woodland with dense underbrush and a body of freshwater.