Diverse genetic biomarkers have been used to evaluate the effects of pollution by mutagenic agents such as metals and pesticides, as well as a large variety of chemical substances derived from human activities. This work researched the effects that an exposure of 60 days to the insecticide Fipronil (concentrations of 0.05, 0.10 and 0.23 μg/L) can cause in the fish Rhamdia quelen using Comet assay with gills, histopathological analysis of gills and the Piscine Micronucleus test and Nuclear Morphological Alterations. The results for the Comet assay and for gills histopathological injuries showed no difference between the control group and the contaminated groups. In the Piscine Micronucleus test, the smallest concentration of Fipronil (0.05 μg/L) was similar as the control group, while concentrations of 0.10 and 0.23 μg/L caused more damage to the DNA. These results suggested that only the highest concentrations of Fipronil tested cause damage in erythrocytes, but none of these concentrations was sufficient to alter the DNA in the gill cells. R. quelen may be a less sensitive bioindicator than other fish that have been tested. On the other hand, the concentrations used may not have been sufficient to detect alterations in the DNA of R. quelen with the chosen tests. Works like this take on great importance given the enormous quantity of substances that are thrown daily into the environment in an uncontrolled way, without evaluation of the consequences. The application of these tests with other concentrations, tissues and exposure times is suggested for future works.