Knowledge of the feeding habit and the digestive physiology of a fish is important in making appropriate strategies for feed development and successful culture. Nutrient-rich small indigenous fish species (SIFs) are abundant in Assam, India. Puntius sophore, Mystus tengara, and Trichogaster fasciata of Gossaigaon, Assam are important SIFs for the local rural population, and also potential candidates for ornamental fish culture. The present study aims to evaluate the feeding habit and digestive enzyme activities of these species. Data obtained from the relative gut length and gut content analysis suggested that M. tengara is a carnivorous fish and the rest two fishes are omnivorous in habit. Further, the relative gut length was highest in T. fasciata (4.20±0.45) and lowest in M. tengara (0.55±0.11). Digestive enzyme activity indicates a correlation with the dietary habit of the fish. Further, total protease, trypsin, and amylase activity was reported highest in P. sophore. Acid protease pepsin was found to be significantly higher in M. tengara complementing its carnivorous habit and gut anatomy. The present study has established some important information on the digestive enzyme characteristics and feeding habits of the three fish species. This information might be useful in the development of suitable feed for the fish species for their culture.