This study investigates the genetic population structures of Plasmodium falciparum isolates from patients with severe or uncomplicated malaria in the Thai-Myanmar border area. Using 12 microsatellite DNA loci, the genetic diversity and population structures of 50 isolates (25 from severe malaria and 25 from uncomplicated malaria) collected between 2002 and 2005 were analyzed. The results showed that the uncomplicated malaria group had greater genetic diversity and effective population size compared to the severe group. Strong linkage disequilibrium was observed in the uncomplicated group, and significant genetic differentiation was found between the two groups. Three of the 12 microsatellite loci showed significant differences in allele frequencies between the groups. The findings suggest that the genetic structures of P. falciparum populations in severe and uncomplicated malaria patients differ. The microsatellite loci used were not related to antigenic features, but some loci may influence clinical outcomes. The study also found that malaria transmission has decreased in the Thai-Myanmar border region in recent years, as indicated by the lower proportion of multi-genotype infections compared to previous studies. The results indicate that genetic diversity is associated with transmission levels in both severe and uncomplicated malaria populations. The study highlights the importance of understanding the genetic structure of P. falciparum populations in different clinical outcomes to better understand malaria pathogenesis and develop effective interventions.This study investigates the genetic population structures of Plasmodium falciparum isolates from patients with severe or uncomplicated malaria in the Thai-Myanmar border area. Using 12 microsatellite DNA loci, the genetic diversity and population structures of 50 isolates (25 from severe malaria and 25 from uncomplicated malaria) collected between 2002 and 2005 were analyzed. The results showed that the uncomplicated malaria group had greater genetic diversity and effective population size compared to the severe group. Strong linkage disequilibrium was observed in the uncomplicated group, and significant genetic differentiation was found between the two groups. Three of the 12 microsatellite loci showed significant differences in allele frequencies between the groups. The findings suggest that the genetic structures of P. falciparum populations in severe and uncomplicated malaria patients differ. The microsatellite loci used were not related to antigenic features, but some loci may influence clinical outcomes. The study also found that malaria transmission has decreased in the Thai-Myanmar border region in recent years, as indicated by the lower proportion of multi-genotype infections compared to previous studies. The results indicate that genetic diversity is associated with transmission levels in both severe and uncomplicated malaria populations. The study highlights the importance of understanding the genetic structure of P. falciparum populations in different clinical outcomes to better understand malaria pathogenesis and develop effective interventions.