Excavation of the new fourth bore of the Caldecott Tunnel in the Berkeley Hills, Oakland, California reveals two faunas attributed to an unnamed glauconitic mudstone (=Sobrante Formation and mapped as Tsm) and the Claremont chert (both of Graymer 2000). The fossil assemblage from the unnamed glauconitic mudstone, referred to here as the Tsm Caldecott Tunnel fauna, consists of 32 taxa: one bryozoan, 22 Mollusca (16 Bivalvia, five Gastropoda and one Scaphopoda), two Arthropoda (one Decapoda and one Maxillopoda), two Echinodermata (one Crinoidae and one Echinoidea), and five Chordata. Mollusks indicate a middle Miocene age based on the co-occurrence of the provisionally identified bivalves Acila empirensis, Anadara osmonti, Yoldia submontereyensis, Y. supramontereyensis and the gastropod genera Bruclarkia and Trophoscyon. This fauna was likely deposited at water depths between 350 and 400 m. Although several taxa from shallower depths are present, these are assumed to have washed in from shallower depths. Only one taxon was found that typically occurs in deeper water. The fauna lived in a methane-rich environment based on the occurrence of vesicomyid bivalves and on a vesicomyid/lucinid bivalve association shown elsewhere to be associated with cold seep environments. Vertebrates include great numbers of small, pelagic fish and the piscivorous sharks and marine mammals which likely took advantage of them for food. The Tsm Caldecott Tunnel fauna represents the second fauna from a methane-rich environment from the greater San Francisco Bay area and the first attributed to a methane seep environment. In addition, this fauna contains the first reported Cenozoic crinoid from California and the new species Dentalium (Fissidentalium?) mcganna (Mollusca: Scaphopoda) is described. The fauna from the Claremont chert includes two bivalve mollusks, one scaphopod, one barnacle and three vertebrates. These taxa are all represented by single specimens. They represent a marine environment likely at continental shelf or slope water depths. The occurrence of the shark Carcharhinus obscurus may indicate water temperatures warmer than off the central California coast today.