Nucleotide sequences of the mitochondrial cytochrome 'c' oxidase subunit 1 ('cox1') gene were used as a "DNA barcode" to identify the closely related species of the ciliate genus 'Tetrahymena ' and 3 other tetrahymenine species. Except for 'Tetrahymena furgasoni, Tetrahymena lwoffi, Tetrahymena pyriformis', and ' Tetrahymena setosa', all isolates could be identified to the species level using 689 bp of the 'cox1' sequences. Intraspecific isolates of 'Tetrahymena borealis, T. lwoffi, Tetrahymena patula', and ' Tetrahymena thermophila' could be discriminated and identified by their 'cox1' sequences as shown by <0.65% intraspecific sequence divegences. However, conspecific individuals of 'T. pyriformis ' and 'Tetrahymena tropicalis' showed high "within-species" sequence divergence values of 5.01% and 9.07%, respectively. Phylogenetic trees constructed using SSUrRNA and 'cox1' nucleotide and amino acid sequences showed the genus 'Tetrahymena' to be monophyletic as opposed to three morphology-and-ecology-based groupings, which are paraphyletic. The SSUrRNA phylogeny showed the 9 previously established ribosets. The 'cox1' nucleotide trees revealed 12 well supported groupings, called coxisets, which mostly corresponded to the 9 ribosets.