Sexual reproduction is a hallmark of most eukaryotes, yet hybridization can lead to alternative reproductive strategies, such as hybridogenesis. During hybridogenesis, found in the European water frog (Pelophylax esculentus) complex, one of the parental genomes is eliminated during gametogenesis, and the other one propagates clonally to gametes. We analyzed diploid hybrid males from populations common for hybrids and Pelophylax lessonae (L-E systems) from the eastern part of their distribution range. All but one hybrid produced spermatocytes and spermatids with Pelophylax ridibundus chromosomes, suggesting premeiotic elimination of P. lessonae genome and endoreplication of the P. ridibundus genome. We also observed spermatocytes with 13 or 26 univalents, indicating alterations in genome elimination and endoreplication. By comparing spermatocytes with germ cell genome composition, we suggest that genome elimination and endoreplication do not occur in adult males. Further, we examined introgressions using mitochondrial and nuclear genetic markers and comparative genomic hybridization. Most hybrids carried P. ridibundus and P. lessonae haplogroups, but five had Pelophylax cf. bedriagae mitochondrial DNA. In one hybrid, we revealed introgression of P. ridibundus chromosomal segments on P. lessonae chromosome. Although L-E systems are generally considered as stable, our results indicate variability in hybrid male gametogenesis, which may be related to introgressive hybridization.