A genetic analysis has indicated that the population of the tertian malaria causative agents Plasmodium vivax in Kyrgyzstan is heterogeneous and consists of various isolates resulting from multiple carriages of the pathogens from the areas of the neighboring countries. Low genetic variability and a weak gene flow between the isolates do not contribute to the establishment of malaria in this area. Experience in controlling the epidemic outbreaks shows that active and residual foci are easily sanitized when antimalaria measures are timely and qualitatively implemented. This creates the necessary for eliminating tertian malaria in the Republic of Kyrgyzstan in the near future.