Release of chemicals and fluctuation in oxygen content in the aquatic environment represent hazards for fish health. The present study aims at assessing the genotoxic impact of low concentration exposures to waterborne uranium (U), dietary methyl mercury (MeHg) and hyperoxia in zebrafish by using the RAPD-PCR quantitative method. A significant increase of the number hybridization sites was observed in fish exposed to 30 μg U/L and 100 μg U/L and hyperoxia. In fish exposed to MeHg (13.5 μg Hg/g, dry weight) no change in the number of hybridization sites were found, however, the frequency of PCR products showed significant variation. The mechanisms of toxicity leading to DNA damage in fish exposed to waterborne uranium, mercury and hyperoxia are discussed and the results from the literature given by the comet assay, micronucleus test and RAPD-PCR method compared. The study provides new data regarding the genotoxic effects of MeHg, hyperoxia and low U concentrations (30 μg U/L) in fish. The present work highlights the use of the RAPD-PCR as a sensitive method in the assessment of chemically-induced DNA damage in animals.