This study investigated the microplastic (MP) contamination of seawater and fishes from different habitats so as to understand the level of human exposure to microplastics. Samples of Harpodon nehereus, Chirocentrus dorab, Sardinella albella, Rastrelliger kanagurta, Katsuwonus pelamis and Istiophorus platypterus were collected from Tuticorin, southeast coast of India. The MPs in seawater and the gastrointestinal tracts of fish were identified using Stereomicroscope and characterized by FTIR and SEM-EDAX analysis. The abundance of MPs varied from 3.1 ± 2.3 to 23.7 ± 4.2 items L−1 in water, from 0.11 ± 0.06 to 3.64 ± 1.7 items/individual, and from 0.0002 ± 0.0001 to 0.2 ± 0.03 items/g gut weight. The epipelagic fishes had higher levels of MP contamination than the mesopelagic ones. Most of the MPs identified were of blue color, of fiber type and with their size <500 μm. Polyethylene was the most commonly detected MP, followed by polyester and polyamide, and this fact could be attributed to the inflow of domestic sewage and to the intensive fisheries activities in the area. SEM-EDAX spectra revealed the weathered MP surfaces which could adsorb/leach inorganic elements (colorants and fillers) from/to the environment. We may conclude that the concentration of MPs in fishes is a function of the concentration of MPs in their environment. Display omitted •MPs were found in coastal waters and in fish gastrointestinal tract.•Higher abundance of MPs was detected in epipelagic fish than in mesopelagic fish.•The most common PE were blue in color, fiber-shaped, and <500 μm in size.•Abundance of MPs in fish was found to depend significantly on the MP pollution in water.