Hydrozoans are widely known for their complex life cycles. The life cycle usually includes an asexual benthic polyp, which produces a sexual zooid (gonophore). Here, we performed an extensive analysis of 183 specimens of hydrozoan genus Sarsia from the White Sea and identified four types of gonophores. We also compared the type of gonophore with haplotypes of molecular markers COI and ITS. Analysis of COI sequences recovered that the studied specimens relate to the species S. tubulosa, S. princeps and S. lovenii, and that S. lovenii specimens divide into two COI-haplogroups. More intraspecies genetic diversity was revealed in the analysis of ITS sequences. Sarsia tubulosa specimens divide into two ITS-haplotypes, and presumably, hybrid forms between these lineages were found. For S. lovenii, we identified 14 ITS-haplotypes as a result of alleles separation. Intra-individual genetic polymorphism of ITS-region is most likely associated with intraspecific hybridization between different haplotypes. The diversity of morphotypes is associated with the genetic diversity of the specimens. Thus, we demonstrated that the morphologically variable species S. lovenii is represented in the White Sea by a network of intensively hybridizing haplotypes. Hybridization affects the morphology and maturation period of gonophores and presumably affects the processes of speciation.