A new species Stenamoeba aeronauta n. sp. was isolated from a culture of large thecamoebids during laboratory studies. Our study of this species showed almost complete morphological identity with the well-known species Stenamoeba stenopodia. Despite the morphological similarity and proximity in the phylogenetic tree, significant differences in the sequence of the 18S rRNA gene forced us to recognize it as a new species. Known species of Stenamoeba have noticeable morphological differences, but the discovery of the new species shows that cryptic speciation appears in this amoeba genus as well as in many others, like Thecamoeba or Vannella. In contrast with many other amoebae genera, the number of available 18S rRNA gene sequences exceeds that of morphologically described isolates. So, it is not yet possible to suggest the application of the names of monophyletic species groups, as it was recently proposed for Thecamoeba species, since every clade of Stenamoeba contains both sequences of species with known morphology and with unknown ones. Overall, the present study further confirms that probably almost all “classical” morphospecies of amoebae may represent a cluster of a sibling species, showing remarkable differences at the molecular level.