Petroleum refinery wastes contain mixtures of toxic compounds including Polycyclic Aromatic Hydrocarbons (PAH) which may pose genotoxic threats to the biota. The objective of the present study was to assess the genotoxic potential of wastewaters of the petroleum refinery at Sapugaskanda, Sri Lanka using erythrocytic micronuclei and nuclear abnormalities as genotoxic biomarkers in the fish Oreochromis niloticus exposed to the refinery wastewater under controlled laboratory conditions and in the field captured fishes from the canals close to the refinery. Erythrocytic micronuclei and nuclear abnormalities in the peripheral blood were evaluated using cytogenetic tests. Patterns of fluorescent aromatic compounds in the fish bile were also examined using fixed fluorescence spectrometry to assess potential PAH exposure. Erythrocytic micronuclei, nuclear buds and notched nuclei in the peripheral blood were highly induced (P < 0.05) in O. niloticus exposed to the wastewater for 7 days under laboratory conditions in comparison to the control fish. The field-captured fishes, Trichogaster pectoralis and Dawkinsia singhala inhabiting water canals near the petroleum refinery also demonstrated significant induction (P <0.05) of erythrocytic micronuclei and other nuclear abnormalities. PAH exposure indicative bile fluorescence patterns (naphthalene, phenanthrene, pyrene, and benzo(a)pyrene types) were detected in the fish exposed to the wastewater under laboratory conditions and in the field captured fishes. The results revealed that the wastewater of petroleum refinery contains genotoxic chemicals including PAHs. Hence, incorporation of genotoxicity tests as bioanalytical tools for regulating the discharge of final refinery wastewater to the aquatic ecosystems would be prudent in consideration of sustainable development goals focusing on the ecosystem and human safety.