The genetic diversity of nine microsatellite loci in three Paragonimus westermani populations, including PwTC, PwTS and Pw-like was studied by means of PCR. The number of alleles was counted, and allele frequencies, polymorphism information content (PIC) and heterozygosity (H) were calculated for each population. The results showed that every microsatellite locus analyzed was polymorphic (≤ 0.95) in these P. westermani populations and all of them were highly polymorphic loci (PIC > 0.5). The average numbers of alleles and PIC in each locus were 12.44 (7 to 19) and 0.739 (0.195 to 0.911), respectively. The average expected heterozygosity in all populations was 0.769, which varied from 0.218 (PwTS) to 0.917 (PwTS). In terms of pairwise distance comparison, all three populations of P. westermani possessed similar genetic distances. However, the populations of PwTC and PwTS possessed the smallest genetic distance of 0.3037.The results from this research were the first report involving a study of population structure at molecular level of P. westermani complex in Thailand.