The identification of effective, nontoxic means for physically marking and tracking marine invertebrate larvae is a necessary step towards meeting a major goal of modern marine population biology, the direct measurement of larval dispersal. An inexpensive, rapid and effective means for marking bivalve larvae would be particularly useful because, as a taxonomic group, bivalves contain many commercially important and exploited species. Likewise, bivalves produce large numbers of propagules for experimental procedures and, for many species, methods for rearing larvae have been well established. Calcein has been used as a marker in numerous studies of adults and juveniles of calcium-carbonate-containing marine organisms, but its effects on small and sensitive life history stages such as embryos and larvae can be detrimental. We show that calcein can be used to rapidly and effectively mark large numbers of larvae from two bivalve species, Argopecten irradians concentricus (Say, 1822) (the Bay Scallop) and Mytilus trossulus Gould, 1850 (the Bay Mussel). Calcein had no detectable negative effects on growth or survivorship of larvae of either species; therefore, this fluorescent mark should serve as a useful tool for directly tracking dispersal of these species in the field. Our marking method is simple and inexpensive and can easily be used to determine the effectiveness and potential toxicity of the calcein mark for other bivalves.