The genus Limnius Illiger, 1802 belongs to the family of aquatic beetles Elmidae (riffle beetles). So far, 14 species distributed in the Palearctic region have been described within the genus, and preliminary molecular analyzes indicate complex systematic relationships that require additional research. In this work I determined the phylogenetic relationships between species within the genus Limnius for samples collected in the Western Palearctic region using the mitochondrial gene COI and the nuclear genes ArgK, H3, CAD and ITS1. Phylogenetic trees were constructed using various phylogenetic methods for individual markers as well as for combinations of marker sets. The results are mostly comparable between the data sets used, but the best resolution is provided using the combined set of all molecular markers. The obtained results confirm previous phylogenetic hypotheses based on morphology about the close relationships of the species L. volckmari / L. intermedius, L. muelleri / L. satanus, L. opacus / L. subopacus and L. perrisi / L. colchicus, but the relationships between the species groups have not been confirmed with certainty. Also, the results indicate the existence of certain species complexes as well as undescribed (cryptic) species within this genus. This research makes an important contribution to the knowledge of systematics within the genus Limnius and represents the basis for future comprehensive taxonomic and phylogenetic studies using an integrative approach.