The parasitic infestation of isopod parasites in the commercially important fish Rastrelliger kanagurta was investigated. Genetic profiling of the Jorymahilsae from Rastrelliger kanagurta was the main aim of the study.The crustacean parasites along the south-west coast of India is high in R. kanagurta. Jorymahilsae occupying the entire branchial chamber of the Rastrelliger kanagurta may produce pressure on the gill surface and thus affect the efficiency of respiration. Although, the infestation does not cause immediate death, it affects the normal growth and appearance of the host fish. This may lead to economic losses among Rastrelliger kanagurta.