Thecamoeba onigiri n. sp. (Amoebozoa, Discosea, Thecamoebida) was isolated from a moss sample collected in the surroundings of Lake Baikal (Russia). The amoebae of this species belong to the striate morphotype and have a single rounded nucleus. The nucleolar material of T. onigiri can be organized in different ways depending on the age of the culture. The most common was a nucleus with a nearly spherical eccentric nucleolus, sometimes located very close to the nuclear envelope. The surface of such a nucleolus was rough and uneven. This type of nucleolar organization was observed in one- to two-week-old cultures. In contrast, a centrally located rounded nucleolus with smooth surface predominated in three- to four-week-old cultures. This type of the nucleolus corresponds to the classical “vesicular” nucleus and is similar to that found in amoebae of “T. quadrilineata species group”, but differs in having lacunae that are more peripheral. Molecular phylogenetic analysis based on 18S rRNA gene sequences showed that T. onigiri forms a clade with T. astrologa as part of a larger group that also includes the “T. quadrilineata species group” and T. aesculea. Meanwhile, two species of Thecamoeba demonstrate polymorphism of the nucleolar material arrangement, and both these species are phylogenetically close.