Vivax malaria occurring in the Republic of Korea is occasionally characterized by a long latent infection induced by hypnozoites in the liver. So far, the mechanisms responsible for short and long latent infections of vivax malaria are not known. Therefore, the present study classified the parasite isolates according to the long and short latent periods and then analysed the genetic diversity of the Plasmodium vivax merozoite surface protein 1 (PvMSP-1). Blood samples containing P. vivax isolates were collected from 465 patients from 2011 to 2013 at health centers in the Republic of Korea. PvMSP-1 gene sequences were analysed in groups classified by the collection year, and short or long latent periods. The samples in short and long latent periods were selected by the timing of vivax malaria occurrence, July-August and January-May, respectively. Three PvMSP-1 types (Sal-1, Belem, and recombinant) were observed in P. vivax isolates collected from 2011 to 2013. Interestingly, the recombinant and Sal-1 types were dominant in vivax malaria of the long and short latent periods, respectively. In addition, the S-b like subtype of the PvMSP-1 Sal-1 type was first identified in 2013. This study revealed that the genetic type of PvMSP-1 is likely related to the duration of its latent period. Moreover, trends of the genetic types of PvMSP-1 seem to be stable in recent years compared with those of previous years in which various new types were observed.