Accurate estimates of reproductive potential are a key component of any stock assessment. Multiple factors influencing the variability in batch fecundity of stone crabs Menippe spp. across the Florida fishery were quantified with a negative binomial regression model. Stone crabs were collected bimonthly from Cedar Key, Tampa Bay, Pavilion Key, and Sawyer Key from April 2013 through April 2015 for fecundity analysis. Batch fecundity (number of eggs per clutch) was estimated by using dry weights. Modeling results revealed that fecundity was strongly and positively related to carapace width and highly variable among locations, months, and years. Batch fecundity was lowest in spring and winter and highest in July and August, which agreed with the general understanding of seasonal patterns in crustacean reproductive cycles. Additionally, batch fecundity was 39% lower for crabs with no claws, indicating that claw removal by the fishery negatively affects reproductive output. Comparisons of estimates from a 1993–1995 fecundity study in Tampa Bay indicated that there was little difference in stone crab fecundity between individuals collected in 1993 and those collected in 2013. But this observed temporal pattern represents observations from only a small portion of the fished population and so may not fully reflect the temporal changes in fecundity occurring throughout the fishery. The present study quantified the spatial and temporal factors influencing variability in stone crab fecundity throughout the fished population of Florida. We hypothesize that spatial differences in food quality, food quantity, and fishing effort may be important drivers of variability in stone crab fecundity. Given the intense harvest and variability in reproductive output, further work should be dedicated to identifying critical spawning and recruitment areas, as well as assessments of their connectivity.