A strain of Vexillifera Schaeffer, 1926 was isolated from the bottom sediments of the Vostok Bay of the Sea of Japan and showed close similarity to V. armata Page, 1979. The new strain shares several morphological characters of this morphospecies, in particular, cell coat structure and the presence of unique “trichocyst-like bodies” in the cytoplasm. The studied strain branches in one of the clades of marine Vexillifera species, with the unnamed Mediterranean Vexillifera strain K9 as its closest relative. Unfortunately, the type strain of V. armata was lost before any molecular data were obtained. Therefore, no information is available on this species for molecular comparison. The studied strain was isolated from the habitat geographically very distant from the type one. The type strain of V. armata was estuarine, while the new strain was isolated from the lower sublittoral benthos and appears to be stenohaline based on the results of an experimental study. It also showed some elusive morphological differences that may be regarded as intraspecific variation. Although currently known extent of cryptic speciation in the naked lobose amoebae is relatively high, the differences between the studied strain and V. armata may be too subtle to warrant a description of a separate species. Therefore, we conclude that the new strain should be identified as Vexillifera cf. armata. Re-isolation of V. armata from its type locality is highly desirable to evaluate a degree of molecular variability within this morphospecies.