Eremias argus and Eremias brenchleyi are lacertid lizards that are sympatric throughout the distribution of E. brenchleyi. We sequenced partial mitochondrial DNA from cytochrome (cyt) b gene for 106 individuals of E. argus from nine localities, and for 45 individuals of E. brenchleyi from five localities, in central and northern parts of North China. We determined 53 cyt b haplotypes from the E. argus samples, and 27 cyt b haplotypes from the E. brenchleyi samples. Only E. brenchleyi had followed a stepping-stone model of dispersal. Partitioned Bayesian phylogenetic analysis reveals that E. argus and E. brenchleyi are reciprocally monophyletic, and the divergence time between the two species was dated to about 4.1±1.2 million years ago. Geographical structuring of haplotypes is more significant in E. brenchleyi than in E. argus. Haplotypes of E. brenchleyi could be divided into four groups by the Yellow River and Taihang Mountains. Within-population genetic diversity indices are correlated neither with latitude nor with longitude. We calculated significant among-population structure for both species (E. argus: ΦST=0.608, P<0.001; E. brenchleyi: ΦST=0.925, P<0.001). Eremias brenchleyi has four independent management units, while E. argus has a more homogeneous genetic structure across its range. Our data show that: (1) the pattern seen in North American and European species that southern populations have higher genetic diversity as consequence of post-glaciation dispersal is absent in the two Chinese lizards; (2) the Yellow River and Taihang Mountains may have acted as important barriers to gene flow only in E. brenchleyi; and (3) genetic structure differs between the two lizards that differ in habitat preference and dispersal ability.