Aquatic insects are particularly dependent on environmental conditions because their life cycles are directly linked to physico-chemical conditions in freshwater habitats. Here, we combine DNA barcoding and ecological analysis to determine general distributional patterns for an unknown fauna of Rhyacophila (Trichoptera, Rhyacophilidae) in the Hengduan Mountains in China. In total 415 larval and 109 adult specimens from four major Hengduan Mountain river basins (1022 m – 4381 m a.s.l.) were sequenced and analyzed. Molecular operational taxonomic units (MOTUs) were delimited as putative species analogs. MOTUs were derived from mitochondrial COI (mtCOI) and nuclear wingless (nuWG) data using the tree-based GMYC method. As expected, based on a higher mutation rate, mtCOI delimitation resulted in a much higher number of MOTUs (66) than in WG (27), but not all mtCOI MOTUs were nested within nuWG MOTUs. Many mtCOI MOTUs were geographically restricted and rare, often occurring in only one or two sampling sites. Multivariate GLM analyses confirmed the importance of basins as the primary factor for explaining the diversity of Rhyacophila MOTUs. The high level of geographical restriction of MOTUs among basins and along elevational gradients indicates that Rhyacophila in the Hengduan Mountains are largely range-restricted, dispersal limited and consequently vulnerable to local changes in environmental conditions.