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Arsenic, the proven genotoxic carcinogen in humans, is a groundwater contaminant of global concern. The present work investigates the applicability of randomly amplified polymorphic DNA (RAPD) as molecular marker to demonstrate arsenic genotoxicity in the freshwater fish, Channa punctatus. Fish specimens, segregated into three groups, were exposed to 10, 50 and 500 µgL− 1 of arsenic respectively for 20 consecutive days. DNA extracted from same specimens of each group before and after exposure was amplified by polymerase chain reaction (PCR) using single arbitrary primers. Marked changes in RAPD profiles of fish DNA were observed upon exposure to arsenic compare to RAPD profiles of their pre-exposure state, resulting from loss or gain of certain bands. Altogether a total of 41 loci were amplified with 37–41 bands in each group. Band 1 of pre-exposure state was lost in all post-exposure samples while bands 4, 6 and 7 appeared as new bands after exposure to arsenic. The changes in the RAPD banding patterns upon exposure to arsenic reflect alterations in fish DNA. The RAPD bands, therefore, appeared as potential markers, capable of revealing the genotoxicity induced by arsenic in this piscine model.