Abstract The taxonomy of the notostracan LepidurusLeach, 1819 is complicated by a large number of synonymised species and extensive intraspecific variability in many relevant characters. We demonstrate, based on an integrative taxonomic approach, that the Ukrainian populations of Lepidurus are not conspecific with any currently accepted Lepidurus species and assign them to the previously synonymised species Lepidurus middendorffiicomp. nov. (Braem, 1893). This species exemplarily highlights the problems in the taxonomy of Lepidurus. The species was originally described as Apus extensus var. middendorffii (Braem, 1893), but L. extensus is a junior synonym of Lepidurus lubbocki (Brauer, 1873), which is currently treated as a subspecies of Lepidurus apus (Linnaeus, 1758). Our molecular genetic analyses based on mitochondrial COI, 12S, 16S, and nuclear 28S, which included published data, suggest the presence of further, possibly cryptic species that await formal recognition and stress the importance for a more extensive revision of Lepidurus. The original type specimens of L. middendorffii, previously stored at the Museum of Natural History (Wrocław University, Wrocław, Poland), are lost and a neotype is designated. Lepidurus middendorffii is characterised by the dorsal organ position between the ocular tubercle margins, the sharp carapace sulcus spines, the long supra-anal plate with many median spines, a telson length to carapace length ratio 0.18–0.35, and differs by > 9% uncorrected COI p-distances from all other Lepidurus species.