In the present study, the seasonal and inter-annual fish assemblage structure of intertidal mudflats of Indian Sundarbans was analysed during tidal cycles. A total of 31 fish species belonging to 22 families and 9 orders were collected during high tide, whereas only 12 were recorded during low tide. Fish assemblage descriptions were based on several community descriptors, namely diversity (H′), species richness (S), species dominance (D), and species evenness (J) and on an ecological guild classification. A canonical correspondence analysis (CCA) was performed to evaluate the relationship between estuarine habitat and fish assemblages in the mudflat habitat during inundated and exposed conditions. All the diversity indices showed marked seasonal and inter-annual variations. Temporal variations were also found in fish assemblage structure in both tidal conditions. Estuarine species were the most important ecological guild of the mudflats during both high and low tides. Of all the abiotic variables examined, CCA showed that salinity, pH and nutrients were the most important influencing fish assemblage during high tide. Total dissolved solids, water temperature and salinity were significant during low tide. Considering the importance of mudflats in supporting fish diversity, the present study emphasizes the increased efforts for conservation of this habitat in the Indian Sundarbans.