Malaria transmission along international borders of the Greater Mekong Subregion is a big challenge for regional malaria elimination. At the Thai-Myanmar border, Plasmodium falciparum cases have dropped dramatically; however, increasing P. vivax prevalence and the emerging reports on hidden malaria burden due to asymptomatic infections demand attention. We conducted cross-sectional surveys to detect asymptomatic malaria infections in a small village located at Thai-Myanmar border and genotyped P. vivax infections in order to understand the level of genetic diversity on such a microgeographic scale. PCR/RFLP and DNA sequencing identified high levels of genetic polymorphisms at both Pvmsp3α and Pvmsp3β loci among P. vivax infections. Combining the PCR/RFLP patterns of Pvmsp3α and Pvmsp3β, a total of 10 genotypes were observed among 17 samples, while concatenated DNA sequences of Pvmsp3α and 3β generated 14 haplotypes with haplotype diversity of 0.97. These markedly diverse parasites on a microgeographic scale suggest the circulation of a considerably large parasite population at the international border.