In this study we describe Rhyacophila siparantum sp. nov., a new species of the Rhyacophila philopotamoides species group from the Bjeshkët e Nemuna Mountains in Kosovo, based on morphological (male adults) and molecular (sequencing of the barcode region of the cytochrome c oxidase subunit I gene (COI)) characteristics. The new species is morphologically closest to Rhyacophila schmidinarica Urbanič, Krušnik & Malicky, 2000, and also closely resembling Rhyacophila hirticornis McLachlan, 1879. R. siparantum sp. nov. differs from both its most similar congeners primarily by the shape of the segment X, which is in lateral view short apically and with a pronounced lateral hump on the posterior edge. This difference, combined with other characters related to the shape of the second segment of inferior appendages, spine pattern of parameres and size of ventral teeth on segments VI and VII, make R. siparantum sp. nov. easily distinguishable from both most similar congeners. Phylogenetic and taxonomic relationships were reconstructed using two methods of phylogenetic inference, and two species delimitation methods. All this supports Rhyacophila siparantum sp. nov. as a distinct taxon. The adults of Rhyacophila siparantum sp. nov. were found during the period May – August, nearby a small rheocrene spring inside a forested area. The new species is most probably a microendemic of the Bjeshkët e Nemuna, a mountainous massive known for several other endemic species of caddisflies. Rhyacophila siparantum sp. nov. is the seventeenth known species of the genus Rhyacophila Pictet, 1834 from Kosovo.