AbstractDaphnia is a good model organism for studying factors affecting dispersal and patterns of genetic diversity. Within this genus, the Daphnia pulex species complex includes lineages from North America and Europe, with some considered invaders in various continents, although their colonization history is poorly known. We used mitochondrial DNA and microsatellite markers to identify the D. pulex complex lineages in Sierra Nevada, determine their reproductive mode and reconstruct their genetic history (over the past ~25 to 65 years). We present the first recording of North American (NA) D. cf. pulex in a European high-mountain lake, showing its arrival ~65 years ago in lake Borreguil without temporal changes in its genetic structure. European (Eu) D. cf. pulicaria is the only lineage present in other Sierra Nevada lakes and also showed no genetic change over time. The results for both species are congruent with obligate parthenogenetic reproduction mode. Moreover, water mineralization may influence the clonal distribution of the D. pulex complex in Sierra Nevada, without ruling out dispersal limitation and/or founder effects. Although NA D. cf. pulex had not spread to other Sierra Nevada lakes, it could threaten Eu D. cf. pulicaria in Sierra Nevada and other European alpine lakes.