Understanding the causes of variation in reproductive output is a major goal of marine metapopulation ecology. Individual reproductive output is often highly variable, and may be dependent on variation in the traits of individuals and qualities of their habitats. Here, we investigate characteristics of breeding habitat, the genetic mating system, and determinants of male mating success in the neon goby Elacatinus lori. This fish is found in close association with the yellow tube sponge Aplysina fistularis in Belize. Females lay eggs inside the sponges of males; males care for the eggs until they hatch. First, we use surveys of sponge size and occupancy status to determine the subset of sponges used by breeding males. We show that breeding males occupy a non-random subset of sponges: sponges occupied by breeding males are larger than those occupied by other residents. Second, we use genetic parentage analysis to determine the mating system. We show that E. lori exhibits a polygynous mating system: some males breed with multiple females simultaneously, sequentially, or both. Third, we use field observations of breeding behavior and measures of male size and sponge size to determine which factors explain variation in male mating success. We show that male size is the primary driver of mating success: male size is significantly and positively related to total reproductive output. This study concludes that large fathers and good homes will contribute to the population persistence of a coral reef fish.