The seasonal fish diversity and assemblages in intertidal mudflats in the Indian Sundarbans were compared between the two tidal phases (high tide and low tide). In terms of number of species per family, Gobiidae was most diverse followed by Engraulidae, Congridae and Muraenidae in submerged mudflats. A total species richness of 31 was recorded in the present study. Two-way analysis of variance was applied to assess the differences in species richness, fish diversity, density and standing stock amongst tidal phases and seasons, while fish assemblage composition was analysed using multivariate analysis (MDS, ANOSIM, SIMPER). The analysis indicated significant fluctuations in fish assemblage during monsoon and post-monsoon seasons supporting specialised and recognisable fish assemblages at low tide. Post-monsoon season, irrespective of tides, was characterised by high species richness, fish density and standing stock. The findings indicated that the intertidal mudflat is a unique system and provides a favourable environment for large variety of estuarine species assemblages. The sustainability of diversified fish assemblages in mudflats depends on constant monitoring and conservation efforts of this unique habitat.