Background: Adverse effects caused by the synthetic pesticides has forced scientists to develop an alternative against the synthetic pesticides. Therefore, it has come a boon to mankind in the form of neem tree having secondary metabolites showing pesticidal properties which is in use since many years. Like neem tree, there has been research done on karanja plant, and its secondary metabolite karanjin has been found to possess good pesticidal properties. Comet assay or alkaline single-cell gel electrophoresis (SCG) was performed in fish Cyprinus carpio after exposure to sub-lethal concentration (0.28 ppm) of karanjin. The assay was carried out in the gill, liver, kidney, and blood. The total DNA content in each tissue was also estimated using Nano Drop. Results: The present study clearly shows that though karanjin is a derived secondary metabolite from plant, it is capable of producing genotoxicity in common carp. As the days of sub-lethal exposure increased, all the four tissues showed decrease in total DNA content which was directly proportional to the formation of DNA comet tails. Conclusion: The use of any kind of plant metabolites in the agriculture and aquaculture farms should be monitored well.