The taxonomic status of the genus Bythotrephes Leydig (Crustacea: Cladocera) has been debated
since the second half of the XIX century. The most widespread view of recent decades has been that
Bythotrephes is a monotypic genus, which was support by preliminary molecular data. However,
the recent detailed morphological revision of this genus clearly distinguishes at least seven species.
Therefore, we performed a multi-lake survey in Central Europe to give new insight into the taxonomic
status of Bythotrephes by combining genetic analysis with traditional morphology-based taxonomy.
Based on the morphology we identified two species in Central Europe, B. brevimanus and B. lilljeborgi,
as well as hybrid forms. For the genetic analysis, we used newly obtained 113 sequences of mtDNA
COI gene of the 535-bp length Bythotrephes from Central Europe and sequences downloaded from
GenBank. There were no significant differences between all analyzed sequences, which supports the
hypothesis that Bythotrephes is a monotypic genus, with only one highly polymorphic species. On the
other hand, the results of our work could point out that the COI gene is insufficient to evaluate the
taxonomic status of Bythotrephes. Nonetheless, we have identified 29 new haplotypes of mtDNA COI,
and one which was the same as the haplotype found in North America and Finland. Furthermore, this
haplotype was the source variant from which most other haplotypes were derived.