In the Laboratory of Parasites of Fishes, Crustaceans and Mollusks (CEPAVE), we undertook a parasitological study on three species of fish from the Espinal and Esteros del Iberá ecoregions of Argentina. Clinostomid metacercariae were found parasitizing Characidium rachovii, Crenicichla vittata and Gymnogeophagus balzanii. In this study, we analysed the damage that these parasites inflict on their hosts through the evaluation of histological sections. In addition, Clinostomum metacercariae were identified using morphological characters and DNA barcoding. In the pathological analysis, we observed that muscle tissue was the most affected. The inflammatory response showed vascular congestion areas and infiltration of numerous inflammatory cells, mainly lymphocytes. The molecular and morphological approach supports the presence of three new lineages of clinostomid metacercariae in Argentina. This could lead to the discovery of a high number of lineages or species of Clinostomum from South America.