Large scale farming of Clarias magur is limited due to non-availability of seed because of the high mortality during larval rearing. The aim of the present study was to develop an optimal dietary strategy for enhancing the larval survival, as the feed has a great influence on the growth and survival of larvae of any fish. Knowledge of ontogenic development of digestive enzymes provides a better understanding of the digestive and nutritional physiology of fish larvae, which in turn helps in the development of suitable feed. To this end, sequences of partial cDNA encoding genes such as amylase, trypsin, pepsin, lipoprotein lipase (LPL), pancreatic triacylglycerol lipase (PL) and bile salt-activated lipase (BAL) were cloned. The experiment was designed for a period of 34 days during which the prevailing feeding schedule was practiced. Significant (P < 0.05) amylase expression and activity was found during the early phase of life cycle till 7 dph (day post hatching) or 9 dph and later declined up to 34 dph. Trypsin expression and activity was detected during the early stages till 16 dph from which pepsin enzyme predominates the digestion of dietary proteins. A variable pattern of expression was found in PL, whereas LPL mRNA expression was significantly high at 16 dph. BAL mRNA expression was also significantly high (P < 0.05) from 16 dph onwards. A similar pattern was observed in lipase activity as that of BAL mRNA expression. The present study would be helpful in designing the feeding strategies and in developing the formulated feed for this fish during its larval rearing which could enhance the survival rate.