Mobile genetic elements (in particular, retrotransposons) constitute a considerable part of eukaryotic genomes. These elements are one of the main sources of variability and instability. Although mobile genetic elements had been discovered more than 60 years ago, certain classes of these elements, such as Penelope-like elements (PLE) remain insufficiently understood. In this work, the results of in silico research into PLE of the S. japonicum genome (one of the most important human parasites from the epidemiological viewpoint) are presented. A new estimate of PLE in the S. japonicum genome was made. It was shown that their high heterogeneity presumably reflects several transposition events. Two groups of canonical PLE copies differing by the amino sequence in the domains RT and EN were found to be present in the Schistosoma genome. The data on the representation, structural features, and possible functional load and evolution of Penelope-like retroelements of the parasite are discussed.