We conducted an integrative taxonomic study of a forest floor dwelling montane rove beetle Quedius obliqueseriatus Eppelsheim, 1889. It is one of many endemic species of the North-Western Caucasus, a region considered a global biodiversity hotspot. Examination of the morphological characters in 93 specimens of Q. obliqueseriatus and phylogenetic assessment of the COI barcode for 28 of them, revealed that this species in fact consists of two distinct (p-distance of 4.0%) allopatric lineages, western and eastern. They subtly differ in the structure of the aedeagus, which was not noticed in the previous revision of this species. Nuclear DNA markers (H3, ITS1, ITS2, Wg and 28S) sampled in both lineages, did not show any divergence. Variation of the non-genitalic morphological characters, such as body size or coloration, is continuous across both lineages. Discovery of microendemic lineages within an endemic rove beetle species highlights how little is understood about the patterns and drivers of endemism in arthropods of the North-Western Caucasus. We refrained from the description of a new species due to shortage of data from the area where newly discovered western and eastern lineages meet. As Q. obliqueseriatus was found to be largely infected with Wolbachia, we gave a review of this infection among insects and other arthropods and its impact on speciation. Finally, we described our method of removal of the Wolbachia COI amplicon by endonuclease restriction enzyme in order to get the desired beetle amplicon from infected specimens.