This study surveyed the genetic differences among Angiostrongylus cantonensis (A. cantonensis) using the mitochondrial cytochrome b (cytb) gene. Partial cytb sequences were determined for 91 worms from eight locations in Thailand. Using morphological techniques, the nematodes were found to be A. cantonensis. Phylogenetic analysis found two main clades, which were subdivided into four subclades (clusters). Haplotype network analysis showed that 11 distinct cytb haplotypes were also present in four groups of A. cantonensis. There was no observable relationship between the genetic differentiation of gene flow and geographical distance. This low genetic variation and geographical distribution of A. cantonensis in each location indicates a founder effect, which may have resulted from multiple independent origins, and suggests that haplotypes migrated from endemic areas via human-related activities.