We examined the phylogeography and the variation of the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit 1 gene (cox1) of the Chinese liver fluke Clonorchis sinensis (Cobbold, 1875) in two geographic localities in the Russian southern Far East and compared them with those from different geographical regions (China, Korea, Japan and Vietnam). The Russian samples differed from those of the other regions in haplotype frequencies, haplotype and nucleotide diversities, and AT/GC ratios. Only 4 of the 18 haplotypes were common to Russian and Chinese samples, and two haplotypes were common to Russia and other regions. The intraspecific genetic distances ranged from 0 to 1.58% for the entire dataset studied and from 0 to 1.25% among the samples from Russia. Phylogenetic trees revealed no significant genealogical clades of samples corresponding to sampling localities and no strong isolation by distance was estimated with Mantel test. Neutrality test analysis suggested a relatively recent population expansion for C. sinensis, whereas goodness-of-fit tests indicated deviation from the strict model of uniform expansion. Therefore, the sequences of the mtDNA cox1 gene provide useful genetic markers for evaluating intraspecific diversity and generating phylogeographic reconstructions for this fish-borne trematode.