It is assumed that the structural complexity of mangroves plays a determining role on sh assemblages in that ecosystem. However, there is limited evidence for how the interaction between the mangroves and environmental variables affects the assemblage structure and composition, abundance and biomass of sh. The main goal of this study was to test whether sh assemblages vary between sectors of mangroves located at different distances from the mouth of the estuary and between root microhabitats and seasons, and to analyze the role of environmental characteristics in these variations. In the Boca del Cielo-San José estuarine channel (Chiapas, Mexico), sh assemblages were sampled during high tide during 2019-2020, within mangroves in three sectors of the channel (lower, middle and upper), while mangrove complexity index, dominance of stilt roots or pneumatophores, litterfall production and six physicochemical parameters of the water were measured. Our results showed that sh assemblages varied signi cantly between sectors, microhabitats and seasons. Lower sector sites dominated by stilt root microhabitats presented the highest species richness, abundance and biomass of sh, while more than 90% of the juvenile sh in the samples were associated with pneumatophores. We found that the interaction of salinity, depth, distance from the estuary mouth, litter production, and dominance of aerial roots or pneumatophores explained patterns of sh abundance and biomass in mangroves. Our observations coincide with other studies in emphasizing the importance of mangroves as nursery and feeding sites for sh, but whose structure is de ned by local variables and factors, which must be taken into account in research and management programs.