Realistic species-specific information about larval life history is necessary for effective management of shellfish and parameterization of larval connectivity models. The patchiness of dispersing larvae, and the resources needed for sorting and identifying them, has limited many studies of larval distribution in the field, especially for species that are less common. In particular, little is known about in situ larval distribution of Pacific geoduck clams (Panopea generosa Gould 1850), a commercially important species found in Puget Sound, WA. A novel approach—time-integrating larval tube traps paired with molecular identification and sorting (FISH-CS)—was used to determine the distribution of geoduck larvae over 4 mo at 3 stations in Quartermaster Harbor. Larvae were found consistently at the surface and thermocline rather than at the bottom. More and larger larvae were captured in the inside and middle of the harbor than the outer harbor, indicating at least some larval retention. Two pulses of larvae were captured, in March and late May to early June. Size—frequency distributions of larvae indicate that these were 2 separate cohorts of larvae, with the possibility of a pulse of larvae from elsewhere toward the end of the season. The only physical parameter associated with relative larval abundance was degree of stratification, although the association was weak. These data represent the first reported study of geoduck larval distribution in the field and the first use of the FISH-CS technique for field collections. In the future, this approach can be used to answer many relevant management questions locally and more broadly, including quantifying larval export from shellfish farms, placement of restoration sites and marine protected areas, and spread of invasive species.