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Background   Plasmodium falciparum  merozoite surface protein-1 (PfMSP-1) and -2 (PfMSP-2) are major blood-stage vaccine candidate antigens. Understanding the genetic diversity of the genes,  pfmsp - 1  and  pfmsp - 2 , is important for recognizing the genetic structure of  P. falciparum , and the development of an effective vaccine based on the antigens. In this study, the genetic diversities of  pfmsp - 1  and  pfmsp - 2  in the Myanmar  P. falciparum  were analysed.    Methods  The  pfmsp - 1  block 2 and  pfmsp - 2  block 3 regions were amplified by polymerase chain reaction from blood samples collected from Myanmar patients who were infected with  P. falciparum  in 2013–2015. The amplified gene fragments were cloned into a T&A vector, and sequenced. Sequence analysis of Myanmar  pfmsp - 1  block 2 and  pfmsp - 2  block 3 was performed to identify the genetic diversity of the regions. The temporal genetic changes of both  pfmsp - 1  and  pfmsp - 2  in the Myanmar  P. falciparum  population, as well as the polymorphic diversity in the publicly available global  pfmsp - 1  and  pfmsp - 2 , were also comparatively analysed.    Results  High levels of genetic diversity of  pfmsp - 1  and  pfmsp - 2  were observed in the Myanmar  P. falciparum  isolates. Twenty-eight different alleles of  pfmsp - 1  (8 for K1 type, 14 for MAD20 type, and 6 for RO33 type) and 59 distinct alleles of  pfmsp - 2  (18 for FC27, and 41 for 3D7 type) were identified in the Myanmar  P. falciparum  population in amino acid level. Comparative analyses of the genetic diversity of the Myanmar  pfmsp - 1  and  pfmsp - 2  alleles in the recent (2013–2015) and past (2004–2006) Myanmar  P. falciparum  populations indicated the dynamic genetic expansion of the  pfmsp - 1  and  pfmsp - 2  in recent years, suggesting that a high level of genetic differentiation and recombination of the two genes may be maintained. Population genetic structure analysis of the global  pfmsp - 1  and  pfmsp - 2  also suggested that a high level of genetic diversity of the two genes was found in the global  P. falciparum  population.    Conclusion  Despite the recent remarkable decline of malaria cases, the Myanmar  P. falciparum  population still remains of sufficient size to allow the generation and maintenance of genetic diversity. The high level of genetic diversity of  pfmsp - 1  and  pfmsp - 2  in the global  P. falciparum  population emphasizes the necessity for continuous monitoring of the genetic diversity of the genes for better understanding of the genetic make-up and evolutionary aspect of the genes in the global  P. falciparum  population.    Electronic supplementary material  The online version of this article (10.1186/s12936-019-2879-7) contains supplementary material, which is available to authorized users.

Changing pattern of the genetic diversities of Plasmodium falciparum merozoite surface protein-1 and merozoite surface protein-2 in Myanmar isolates