Hatcheries providing seed for bivalve mollusc aquaculture can suffer from disease outbreaks resulting in high losses of larvae. Previous research demonstrated the effectiveness of candidate probiotics Phaeobacter inhibens S4 (S4) and Bacillus pumilus RI06-95 (RI) in protecting the larvae of eastern oysters Crassostrea virginica, against bacterial challenge. In this study, the ability of this probionts in protecting larvae of other bivalve species, including northern quahog Mercenaria mercenaria, bay scallops Argopecten irradians, blue mussels Mytilus edulis, and razor clams Ensis directus, was investigated. Pretreatment of larvae with 106 colony forming units /ml probiotic S4 and a mixture of S4 and RI protected bay scallop larvae [relative percent survival (RPS): 69% ± 4%]. In pilot-scale hatchery trials, daily additions of candidate probiotics to the water of static tanks containing northern quahog or bay scallop larvae had no significant impact on larval growth and survival. Daily treatment of tanks with the probiotic RI led to significantly lower levels of Vibrio spp. levels in water and larvae compared with control on day 8 of the northern quahog hatchery trial (P < 0.05), but not for the bay scallop trial. Exposure of bay scallop larvae to S4 and a mixture of S4 and RI in the hatchery provided partial protection to experimental challenge (RPS: 55% ± 14% and 54% ± 4%, respectively). Treatment of northern quahog larvae with probiotics in the hatchery did not lead to increased protection to bacterial challenge. These candidate probiotic strains appear to have species-specific protective effects for bivalve larvae.