Background and Aim:Parasitic infection commonly affects freshwater ornamental fishes. Parasites in fish may impede their growth and even cause death, resulting in a decline in fecundity. The prevalence of lernaeosis in aquaculture ponds in Indonesia requires attention because of missing data, especially from Yogyakarta. Therefore, this study aimed to identify theLernaeaspecies found in fish in Indonesia, particularly in Yogyakarta, molecularly and morphologically, as well as an overview of their distribution and the water condition they inhabit.Materials and Methods:Lernaeaspecies were collected from three different fish species in two districts of Yogyakarta, Indonesia, for precise identification.Lernaeaspecimens were characterized morphologically and subjected to molecular identification based on18S rRNAand28S rRNAgenes.Results:Lernaeain this study was morphologically and genetically confirmed asLernaea cyprinacea, and the infection rate in each fish species was different. Water conditions might have contributed to the differences in infection levels.Conclusion:This study characterizedL. cyprinaceaisolated from Yogyakarta. Future research should focus on sequencing as much molecular information as possible and carrying out more experimental infections.