BACKGROUND: The genetic diversity of malaria parasites varies between regions in the world. The genetic polymorphisms of the genes Pvs48/45 and Pvs47 which encode gametocyte/gamete proteins of Plasmodium vivax, were studied because of their potential as transmission-blocking vaccine (TBV) targets. The aim of the present study was to investigate the genetic diversity of Pvs48/45 and Pvs47 in clinical isolates from endemic areas of Thailand. METHODS: Plasmodium vivax samples collected from four provinces neighbouring either Myanmar or Malaysia were analysed using polymerase chain reaction and nucleotide sequencing.   RESULTS: Fifteen and 18 amino acid substitutions were observed in 36 Pvs48/45 and 62 Pvs47 deduced amino acid sequences, respectively. Eleven haplotypes were identified in Pvs48/45 and 26 in Pvs47. Overall, low nucleotide diversities were observed for Pvs48/45 (π = 0.00104) and Pvs47 (π = 0.00321). Tajima's D, and Fu and Li's D* and F* values were negative for both genes, Pvs48/45 and Pvs47 while a significant difference was found in Pvs48/45 (P < 0.05). CONCLUSION: The limited polymorphism of the two investigated TBV candidate antigens observed in this study is consistent with findings in worldwide isolates. The collected genetic diversity data could be helpful for developing effective TBVs in malaria-endemic areas.