To determine the role of mangroves for fisheries in the arid region of the Persian Gulf, we investigated fish community structure and trophic diversity in intertidal creeks with and without mangroves. Fish community abundances and biomass were compared across habitats and seasons. To identify variations in overall community trophic niches among habitats and seasons, we measured niches with size-corrected standard ellipse areas (SEAc) calculated from C and N stable isotope values. Although there was a slightly greater species richness occurred in mangrove creeks, we found a general similarity in the diversity patterns in creeks with and without mangroves. Also, there were no consistent differences in fish abundance or biomass for mangrove vs. non-mangrove fish collections. Community trophic diversity measured as SEAc also showed no significant difference between mangrove and non-mangrove sites. Instead, strong seasonal patterns were observed in the fish assemblages. Winter samples had consistently higher fish abundance and biomass than summer samples. Winter SEAc values were significantly higher, indicating that the fish community had a larger isotopic niche in winter than summer. Overall, we found that seasonality was much stronger than habitat in determining fish community structure and trophic diversity in the mangrove and non-mangrove ecosystems of Qeshm Island, Iran.