The presence of four taxa at the species and subspecies level was revealed based on morphological investigation of a small collection of the representatives of the genus Bythotrephes Leydig, 1860 from Austrian subalpine lakes. The presence of a new species, B. inexpectatus sp. nov. was revealed in two lakes and the presence of a new subspecies, B. longimanus austriacus ssp. nov., in six lakes. Specimens of the population from the Lake Halstättersee, distinguished by the presence of peculiar features, are provisionally assigned to the species B. brevimanus Lilljeborg, 1901 of which the main range is confined to Circumbaltic region. Few morphologically specific specimens from Wolfgangsee could not be accurately identified and therefore assigned to the taxon Bythotrephes sp. requiring further investigation. Previously described taxa from the region, B. styriacus Ischreyt, 1939 and B. longimanus var. carnica Ischreyt, 1939, were considered either required further taxonomic evaluation or having an unclear taxonomic status, respectively. In one lake, the co-occurrence of two species was recorded, which is a rather rare case for the representatives of the genus. The potential reasons for the high species richness of spiny waterfleas in Austrian subalpine lakes and their possible origin are briefly discussed.