The fishing cat (Prionailurus viverrinus) is a medium-sized wetland specialist threatened felid with limited knowledge base on behavior and ecology. We carried out comprehensive analysis of its diet within a human-dominated landscape in southern Nepal, analyzing scat samples through microscopic analysis and DNA metabarcoding. The microscopic analysis revealed that mammals, primarily rodents, constituted the largest proportion of fishing cat diet (61.73% frequency of occurrence (FO)) followed by birds (43.21% FO) fish (24.69% FO) and reptiles (19.75% FO). However, DNA metabarcoding documented fish as the main diet (70% FO), followed by mammals (63.33% FO) and birds (30% FO). Our findings demonstrate that, fish alone is not a major food source of fishing cats indicate their role to regulate rodents and birds that damages the farm crops. The trophic niche breadth (0.68) shows the fishing cats a diet generalist. We recommend launching awareness programs and programs promoting integrated fish cum paddy farming among fish farmers within the fishing cat range, benefiting both farmers and fishing cat populations. Additionally, targeted conservation measures such as controlling physical and chemical pollution in agricultural and wetland sites are essential to mitigate threats to fishing cat populations. Prioritizing wetland health should be a central strategy in conservation efforts, which will benefit not only fishing cat, but also many co-distributed species.