Species of the Paramecium aurelia complex show diff erent levels of intraspecific polymor phism, with P. dodecaurelia revealing a high level of intraspecific variation. Paramecium dodecaurelia strains originating from distant localities in the Palaearctic, Nor th America ( USA), and Oceania (Hawaii) were studied in ter ms of i ntraspecific diff erentiation and t he deg r ee of speciation. Sequences of genes encoding the ITS1–5.8S-ITS2–5’ end of L SU rDNA (1063–1097 bp) and cytochrome c oxidase subunit I mtDNA ( 638–644 bp) were obtained from 33 s trains of P. dodecaurelia,other P. aurelia species, and another s pecies of the genus Pa ra mecium, with Tetrahymena sp. used as an outg r oup. In phylog rams, t he majority of P. dodecaurelia strains from the Palaearctic appear in one cluster, while strains from J apan, Hawaii and the USA are g rouped in another cluster, together with some strains from I taly and r epresentatives of the P. aurelia species complex. Our r esults tend to suppor t t he hypothesis t hat P.