Macrohectopus branickii is the only pelagic amphipod from Lake Baikal. Until now, despite the uniqueness of M. branickii, its genetic diversity at the intraspecific level, as well as its intraspecific morphological diversity, have not been studied. In this work, we present the result of a morphological analysis of intrapopulation variability of the species M. branickii from the northern basin of Lake Baikal, as well as the result of a molecular analysis based on the sequence of a fragment of the mitochondrial Nad5 gene of several individuals of this species from three basins of the lake. The material for the study was collected using a plankton net and trawl from all basins and shores of Lake Baikal at depths of 100-300 m. We measured 21 morphological characters according to the scheme previously proposed in Tikhonova’s work for sexually mature females of M. branickii living on different shores of the northern basin of Lake Baikal. The coefficient of variation of the values of all characteristics was determined. Morphological analysis revealed different degrees of variability in the studied characters for M. branickii. The most variable characters are: the length of 1 segment of the peduncle of the upper antennae; length of 4 and 5 segments of the stalk of the lower antennae; length of gnathopod propodites 2 pairs; width and length of basipodites of the third pair of pereiopods; length of the stalk, external and internal branches of the uropods of the third pair; telson width and length. Analysis of the nucleotide sequences of the Nad5 gene fragment showed their low variability. The haplotype network was reconstructed using the pegas package for the R programming language. M. branickii forms a single panmictic population, consistent with the absence of geographic and environmental barriers in the pelagic zone of the lake.