The results of the internal transcribed spacer (ITS2) of extrachromosomal rDNA and the chloroplast SSU rDNA sequence analysis presented here confirmed elevated genetic polymorphism revealed earlier by RFLP and RAPD for seven clones of the cosmopolitan species - <em>Euglena agilis</em> Carter. High diversity among these clonal strains was not reflected by morphological criteria, with the exception of the only one character - the ability of the cell in its non-motile dividing states (palmella) to produce mucus and form a slimy envelope. Evolutionary adaptation as formation of slimy envelope may be attributed to different survival strategy of the species by which it adapts to life in a highly variable environment.