The work presents the results of comparative studies of the morphology and genetics of the Baikal subendemic – the harpacticoid copepod Harpacticella inopinata Sars, 1908. The material was obtained from the southern part of Baikal Lake and the Yenisei River within the of Krasnoyarsk city in 1969, 2017–2022. It is shown that morphological variability within the species appeared most in the structure of the antenna exopodite, the number of pores and sensillas on the integument of thoracic somites. The genetic variation of the studied sample of H. inopinata was described by four clades with a distance between them of 0.26, the genetic distances between individuals within the detected genetic groups did not exceed 0.005. It was determined that H. inopinata from geographically remote habitats (Baikal Lake and Yenisei River) forms a single morphological and genetic group. Analysis of the genetic diversity of H. inopinata confirms the relatively recent Baikal origin of the species in the Yenisei, probably associated with an anthropogenic moving into the river.