Digeneans (Trematoda: Digenea) are endoparasites that present a complex life cycle, generally involving an intermediate invertebrate host and a vertebrate host. There is limited information about which species of molluscs may act as intermediate hosts in the upper Paraná River floodplain (UPRF), where Aylacostoma chloroticum can be considered a potential candidate. The study of digeneans in this region is important because some of these parasites are potentially zoonotic, and, therefore, are relevant to public health. However, the correct identification of these organisms during the larval stages is difficult because of the lack of morphologically diagnostic characteristics. The objective of this study was to identify and molecularly characterize the larval stages of digeneans found in A. chloroticum in the UPRF, using the mitochondrial marker of subunit I of cytochrome c oxidase and the 28S nuclear marker. The molluscs were examined in the laboratory and three morphotypes of cercariae were found. DNA was extracted from the specimens obtained and was then amplified and sequenced. The morphotypes exhibited high genetic similarities with Pseudosellacotyla, Paralecithodendrium and Philophthalmus, indicating that these organisms belong to these genera. This is the first record of larval stages of these genera in molluscs collected in the UPRF.