Abstract The inadequate choice of a diagnostic method or the option for techniques that have low sensitivity and specificity may limit the diagnosis of parasitic agents that affect aquatic mammals. The aim of this study was to evaluate the performance of the FLOTAC technique and compare it with three traditional methods (Willis, sedimentation and centrifugation- flotation) used in the diagnosis of gastrointestinal parasites in aquatic mammals. For this, 129 fecal samples from 12 species were collected. Each sample was submitted to laboratory processing using the Willis, Hoffman techniques, Faust method and FLOTAC. Sensitivity, specificity, real prevalence, estimated prevalence, positive predictive value, negative predictive value, correct classification (accuracy) and incorrect classification were evaluated to compare the different diagnostic methods. The highest frequency of positive samples occurred using FLOTAC (46.51%), compared to Hoffman (23.25%), Faust (10.07%) and Willis techniques (6.97%). In the samples analyzed, the occurrence of Strongylidae eggs and Eimeriidae oocysts was frequently observed. The FLOTAC technique proved to be the most appropriate technique and due to its efficacy, is strongly recommended for coproparasitological evaluations in aquatic mammals.