Abstract Determination of total antioxidant capacity, instead of the measurements of limited number of antioxidants, is very important for the understanding of how antioxidants interact with reactive oxygen species (ROS). Several techniques already exist with this propose, although some of them are extremely time-consuming. A new methodology is proposed, based on the detection of ROS by fluorometry (ex/em: 485/520 nm) employing 2′,7′-dichlorofluorescein diacetate (H 2DCF-DA) as substrate. Supernatant of homogenized samples from different organs (gill, muscle, liver, and brain) of the teleost fish Jenynsia multidentata (Anaplebidae) were exposed to peroxyl radicals generated by thermal (35 °C) decomposition of 2,2′-azobis (2 methylpropionamidine) dihydrochloride (ABAP, 4 mM). Different protein concentrations (0.5, 1, 2 and 8 mg/ml) were assayed to get the best signal and curve fitting of fluorescence data over time (30 min). Total antioxidant capacity against peroxyl radicals was estimated as the difference in ROS area with and without ABAP, relative to the fluorescence registered without ABAP. For application of this methodology, J. multidentata specimens were exposed for 24 h to microcystins, cyanotoxins known to induce oxidative stress. Almost all organs showed a lower antioxidant capacity ( p < 0.05) in samples with 8 mg proteins/ml, when compared to protein content of 1–2 mg/ml. In liver samples, higher ( p < 0.05) free iron content was determined in samples with 8 mg proteins/ml. Sensitivity test employing GSH spiked in homogenized samples showed the protocol efficiency in detecting total antioxidant capacity. In the test with microcystins a dose-dependent decrease ( p < 0.05) of antioxidant competence in gills and brain and an inverse result with liver samples were observed. The use of antioxidant defenses was efficient in avoiding oxidative damage, as the content of oxidized proteins was not altered. Data obtained show the potential of this new methodology to be used in ecotoxicological studies.