Resumo. Abstract: Aim This study pursued the detection of cyr and mcy genes to assess the presence of cylindrospemopsin (CN) and microcystin (MC) potential producers in Ecuadorian water bodies. Methods Environmental DNA (eDNA) was extracted from eight water bodies and one wastewater treatment plant (WWTP) from Ecuador. A nested PCR was designed to amplify mcyB, cyrE, and cyrJ genes in these environmental samples. PCR products were sequenced and blasted against GenBank database. Results Potential CN producers were found in seven water bodies and the WWTP. cyrE amplification revealed three variants belonging to Raphidopsis and Aphanizmenon species and one for cyrJ with around 90% identity with Raphidiopsis and Oscillatoria species. Four water bodies presented the same variant for mcyB similar to Microcystis panniformis with 99% of identity. Conclusions This study contributes new data on the presence of toxic cyanobacteria strains and provides new molecular tools to assess cyanotoxin hazards in Ecuadorian water bodies.