Argulus is one of the most important fish parasites that cause heavy economic loss to aquaculture industry. The present investigation was undertaken to study the genetic diversity of the Argulus sp. collected from 13 locations representing major aquaculture zones in India by RAPD analysis and to develop species-specific markers. Thirteen random decamer primers were used to amplify DNA fragments from three individual parasites of each location. Of the 172 bands scored by the primers, 168 were polymorphic. The per cent polymorphic loci and gene diversity values varied within a range of 8.14–43.02 and 0.0342–0.1727 respectively. Nei's genetic similarity between populations across all the primers ranged from 0.363 to 0.969. The dendrogram based on Nei's genetic distance showed two clusters; Bangalore and Mandi populations forming one cluster, and the rest in another cluster. The clusters also revealed strong correlation with the species identified as A. japonicus and A. siamensis respectively by morphological method. The study thus indicated A. siamensis as the major prevalent species in carp culture farms in India. Species-specific primers were designed from unique sequences cloned from RAPD fragments that could able to identify A. siamensis and A. japonicus separately.