Aquaculture of the geoduck, Panopea generosa Gould, 1850, has increased dramatically during the past decade in southern Puget Sound, WA, and the effects of these intertidal aquaculture geoduck beds on local fauna is mostly unknown. This study examined the species composition, relative abundances, and biodiversity indices of mobile benthic fauna in geoduck farm areas of southern Puget Sound. Surveys of geoduck farms in two different stages of aquaculture production were carried out using a trapping strategy with two types of traps. The site in Eld Inlet had predator protection tubes around the planted geoduck. The site in Nisqually Reach was in grow-out phase with no predator protection. Nearby areas with no aquaculture were used as control sites. Traps yielded 1,161 individuals from 15 species of mobile benthic animals during the course of this study. The graceful crab, Cancer gracilis, accounted for 76.3% of all specimens. The effects of geoduck aquaculture on biodiversity were subtle and not consistent between the two locations. Using Coleman rarefaction analysis, species richness was significantly higher (P < 0.05) in the geoduck farm in Eld Inlet compared with its control site, but no significant difference was observed in species richness between the geoduck farm in Nisqually Reach with its control site. Biodiversity was higher in Nisqually Reach compared with Eld Inlet, and Simpson's biodiversity index for the Nisqually Reach geoduck farm was significantly higher than its control site (0.73 and 0.62, respectively, P = 0.001). Large differences in capture rates were noted between female and male Cancer gracilis crab in Eld Inlet and Nisqually Reach. Possible causes of the observed differences between the sites are discussed.