European mountains are important areas regarding biodiversity of the continent, and they also harbour diverse freshwater fauna, which is critically endangered in terms of the current species extinction. However, sufficient knowledge of this valuable part of European biota is no longer possible without molecular data. This study focuses on the genetic diversity and distribution patterns of the classical representative of the mountain freshwater fauna, caddisfly Rhyacophila tristis, in the Western Carpathians. Based on the COI mitochondrial marker, two genetic lineages (separate BINs) were identified. BIN_W was found in 16 localities in the western part of the study area, BIN_E in 44 eastern localities. The data obtained indicate that BIN_W occurs in a significantly narrower altitude range, BIN_E is more closely related to the Balkan populations than to co-occurring BIN_W, and that the contact zone of the lineages passes through the Western Carpathians. The study revealed phylogeographic and demographic differences between lineages, supporting hypothesis of their evolutionary independence and specific ecological preferences. The obtained genetic data shifted our knowledge on the populations of the studied caddisfly and suggested patterns that could be common to other freshwater species. This could help us to protect unique freshwater ecosystems and preserve European biodiversity.