Whereas diel fish migration between mangrove and seagrass habitats has been recognized for decades, quantitative studies have focused mainly on diurnal patterns of fish distribution and abundance. In general, previous studies have shown that fish abundances decline with increasing distance from mangroves; however, evidence for such a pattern at night, when many fishes are actively feeding, is scarce. The present study is the first to report nocturnal fish abundances along a continuous distance gradient from mangroves across adjacent seagrass habitat (0–120 m). Here, we used nocturnal seine sampling to test the null hypothesis (based on diurnal studies and limited nocturnal work) that fish abundance would decrease with increasing distance from shoreline. We focused on species and life-stage-specific abundance patterns of Lutjanus griseus, Sphyraena barracuda, Archosargus rhomboidalis, and Haemulon sciurus. Results indicated that assemblage composition and structure differed significantly by season, likely influenced by temperature. However, within each season, the fish habitat use pattern at both the assemblage and species-specific level generally failed to support our working null hypothesis. Species-specific analyses revealed that, for most species and life-stages examined, nocturnal abundance either did not change with distance or increased with distance from the mangrove-seagrass ecotone. Our results suggest that analyses where taxa are grouped to report overall patterns may have the potential to overlook significant species- and stage-specific variation. For fishes known to make nocturnal migrations, we recommend nocturnal sampling to determine habitat utilization patterns, especially when inferring nursery value of multiple habitats or when estimating fish production.