The morphospecies concept, routinely applied for amoebae, was almost satisfactory when most of studies were limited to ecological, faunistic and taxonomic purposes. Molecular biological tools, applied in order to increase the resolution of species distinction, show that genetic structure of amoebae morphospecies is rather complex. To challenge the problem we performed wide-scale studies of several widely distributed amoebae species belonging to the genera Vannella, Korotnevella, Flamella and Cochliopodium. Cox I gene and portions of 18S r DNA genes were used as a DNA barcode; amoebae were sampled in many regions around the world and sampling sites were located at the distances from several meters to several thousand kilometers from each other. Results were congruent for all studied species and genes and indicated that: (1) properly defined amoebae morphospecies represents genetically distinct unit (2) an amoeba morphospecies consists of limited set of genetic lineages (phylotypes) forming monophyletic clade i