The marine ecosystem is constantly threatened by a wide variety of anthropogenic hazardous chemicals, such as, heavy metals, pesticides, oil, petroleum hydrocarbons, etc., from industries, agricultural sources and sewage disposal. Pakistan, being a country with agriculture prominence, uses pesticides widely for crop protection, and thereby suffers from pollution. In the present study, we assessed a few biomarkers as indicators of the genotoxic chemicals, pesticides and herbicides. We inducted micronucleus (MN) in the gill tissues of green mussel Perna viridis (L.) exposed to different concentrations of organo-phosphate pesticides (chlorpyrifos, malathion) and synthetic pyrethroid pesticides (cypermethrin, lambda-cyhalothrin) and a herbicide (buctril). The MN frequencies of the pesticides treated mussels were observed to increase significantly (P < 0.05) in a dose-dependent manner at all exposure periods. The highest MN frequencies were recorded in gill tissues of cypermethrin treated mussels on the 12th day (10, 11.5 and 13.5 parts per thousand at 0.5, 1 and 1.5 ppm, respectively). The genotoxic effect of pesticides on Perna viridis (gill tissue) was in the following order cypermethrin > chlorpyrifos > malathion > lambda-cyhalothrin > buctril.