The genus Daphnia O.F. Mueller, 1776 (Crustacea: Cladocera: Daphniidae) holds a prominent place among the iconic model organisms in modern biological science. At the same time, it is a well-known example of a genus with a complicated and often confused taxonomy, for which there are multiple objective and subjective reasons. Such confusion is specially obvious in the Daphnia (D.) pulex group, specially D. pulex complex within the latter, despite its species being numerous, globally distributed, and ecologically significant. We had an opportunity to annotate a mitogenome of D. titicacensis Birge, 1909 from Lake Titicaca and discuss the evolutionary history of this group based on new genomic data. We found that: (1) The D. pulex complex is subdivided into D. pulex s.str., "European D. cf. pulicaria", D. titicacensis and D. pulicaria species flock. These four portions of the complex are clearly subdivided by the barcoding gaps, first three ones represent "good" biological species. D. titacacensis is a distinct, and already named, South American species found in high mountains of Peru and Bolivia. (2) There are no barcoding gaps within the D. pulicaria species flock. Theoretically, whole this assembly could be regarded as belonging to a single species D. pulicaria Forbes, 1893 in terms of the COI-based delimitation, all others are junior synonyms of the latter. In our understanding, to date it is better to speak about a "species flock". (3) Our phylogenetic trees and the haplotype network do not support the version of a Southern American origin of D. pulex complex, as well as of the D. pulicaria species flock (Mergeay et al., 2008). Version about the Nearctic origin of the flock (Crease et al. 2012) agrees with our data. Unfortunately, taxonomy of the D. pulex complex still remains to be dubious. We need to continue efforts to resolve numerous problems concerning the former combining different approaches, from genomics to morphology and ecology.