Aim of the study This research article examines the zootherapeutic uses of fish, shellfish and some other aquatic animals in two fishing villages in Bangladesh-one floodplain and one coastal. Materials and methods The floodplain fishing village Volarkandi is located within the Hakaluki wetland ecosystem in the northern Bangladesh and is inhabited mostly by Muslim fishers, whereas the coastal fishing village Thakurtala is located on Moheskhali island and most of the inhabitants are caste-based Hindu fishers. Participatory techniques were used to collect and validate information from the key informants. Results The research revealed that, historically, fishers have used fish and other aquatic animals not only as food items for nutrition, but also to solve a host of physical problems and diseases. Fish and shellfish are widely used for their galactogogue and aphrodisiac properties, for quick recovery from long-time sickness, to enhance the ‘intelligence level’ of children, and to prevent and treat a host of diseases like night blindness, chicken pox, dysentery, piles, muscular inflammation, fistula, malaria, skin diseases and ‘big belly’ syndrome in children. Depending on the objective of the use, different parts of the animal body, its derivatives, or the whole animal are used. The research also clarified different forms of the recipes used. The socio-cultural construction of the ethnomedicinal uses and the distinct gender roles of the fisherwomen were analyzed. Conclusion The research revealed that the aetiologies and the preventive measures against folk illness are socio-culturally embedded and such indigenous medical systems grow and are sustained as a situated body of knowledge within the boundaries of a typical world view framed by local culture and biodiversity.