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Impact of microplastic pollution on the marine environment and its biota is a major concern globally. Gulf of Mannar (GoM) and Palk Bay (PB) are two important biodiversity hotspots along the south-east coast of India. However, in the recent years the intense tourism and fishery activities have made the ecosystem and biota of these two ecologically significant coastal zones vulnerable to microplastic contamination. Hence, a comparative study on the seasonal distribution of microplastics in the surface waters, sediments, and in commercially important fishes were conducted to evaluate the threats imposed by microplastics on the environment and biota of both these coastal ecosystems. Microplastic distribution in the surface waters and sediments of GoM and PB exhibited conspicuous seasonal variation and showed positive correlation with the seasonal current patterns. In the surface waters of GoM, microplastics were abundant during the South West Monsoon whereas in PB it was high during the Early Winter Monsoon period. In the sediments of PB, microplastics was more during Spring Inter-monsoon and South West Monsoon whereas in GoM it was high during Late Winter Monsoon. Fragments, of size 1 to 5 mm formed the abundant microplastic type in the surface waters whereas in the sediments, fragments of size < 1 mm dominated. Of the gut content of the 613 fishes belonging to 12 families examined, microplastics were more in pelagic than demersal fishes with higher incidences in the family Clupeidae (42%). Among the fishes studied, microplastic ingestion was more in Selaroides leptolepis (27.77%), Sphyraena sp. (14.28%), Pelates quadrilineatus (12%), Caranx sp. (10.34%), and Sphyraena barracuda (10%).