Malachite Green (Basic Green 4) is basic, water soluble dye, used as biological stain and mostly used in aquaculture practices as antiparasite, antihelmenthes and antifungal but excess dose is cytotoxic and mutagenic. In present study, the first report of histopathological and genotoxic effects of Malachite green in bivalves for acute exposure were studied. Exposure to acute dose of Malachite green for 96 hours showed harmful action in the bivalve Lamellidens marginalis. Histopathological investigations were conducted in gill, hepatopancrease and gonad in 0.3ppm and 0.9ppm concentration compared to control bivalve. In gill, changes were observed as rupture of epithelial cells, vacuolisation, damaged cilia, fused gill lamelle and formation of granuloma. Like gill, in hepatopancrease the structural changes i.e breakdown of basement membrane, digestive cells changed their normal shape get distorted, vaculisation, karyolysis and necrosis were noticed. The female gonad of bivalve showed degeneration of follicle wall with less number of developing oocyte, severely damaged vitellogenic and previtellogenic oocyte and mixing of cellular content of oocyte. The comet assay was recorded in gill cells at both the exposure. The tail DNA % and tail moment was more significant in 0.9 ppm concentration. The results indicate that the histopathological alterations and genotoxic assessment in the organs of Lamelliden marginalis as reliable biomarker in biomonitoring of Malachite green toxicity in aquatic ecosystem.