The ant species, Vollenhovia emeryi, is distributed in Far East. The species can be divided into two major groups by their wing morphology of reproductives: short-winged and long-winged. A nationwide survey of the species was conducted for analyzing the mitochondrial haplotype diversity and genetic population structure. We collected 91 samples from 40 locations. A total of the 1239 bp partial COI (cytochrome C oxidase 1) region was used for the analyses. We found the total of 21 haplotypes. The mitochondrial haplotypes may correspond to the wing morphology. The genetic population structure examined potential geographic barriers of gene flow such as distance, mountains, rivers and plains which are non-mountain areas to prevent dispersal through mountain range. The result implied that no barriers considered in this study affected differently gene flow. Therefore, the behavioral characteristics of the ant may be the causal constraint of its genetic exchange.