The Westernmost Mediterranean Basin (WMB) can be divided into four geological regions:  Rif, Betic, Transitional and Iberian. Its high biodiversity is likely a result of geological processes and dramatic climatic changes (e.g. Mediterranean climate, ice ages). We aim to unravel the phylogenetic and ecological basis of current patterns of Hydropsyche species diversity in WMB. Two hypotheses may explain these patterns: (1) ecological restrictions to gene flow between populations acting along the stream, which ultimately lead to separate species, or (2) vicariant events associated to the formation of the four regions. The first hypothesis predicts that species with close ecological preferences will form monophyletic groups, the second that major clades will each be confined to a single geological region. To test them, we collected data on Hydropsyche species and environmental variables and sequenced mitochondrial and nuclear genes belonging to 19 species. Ecological and phylogenetic analyses grouped species into three main ecological categories (headwaters, midstream and downstream) and found low levels of species co-occurrence at local scale. Our data suggest that diversity patterns of Hydropsyche in WMB are better explained by ecological niche conservatism than vicariant events, while competitive exclusion may have played an important role on species distribution at local scale.