We report concentrations of methylmercury (MeHg) and total mercury (THg) in marine, freshwater and aquaculture species from a major fisheries landing center in the east coast of India, Nellore. Concentrations of MeHg were in the range 1.67–105.25 ng/g ww (wet weight). Aquaculture species had lower mercury concentrations than naturally caught marine or freshwater species (p < 0.05). While none of the 242 analyzed samples had MeHg greater than the limits stipulated by food and safety authority in India (250 ng/g) or other countries, dietary exposure analysis for a subsistence fish consuming Indian population for which fish consumption patterns were known revealed that there was a 14.3% probability of exceedance of the US EPA reference dose of 0.1 µg/kg BW/day. The US EPA one-box pharmacokinetic model slightly better predicts the observed hair mercury concentrations in this population when the MeHg absorption efficiency in the human gastrointestinal tract is 1–72% (with a median of 14%) as suggested recently rather than the 91–97% used more commonly. © 2020, Springer Nature B.V.