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Therefore, tracing the origins of new malaria infections is important in the maintenance of malaria-free zones in this border region. A new genotyping tool based on a robust mitochondrial (<jats:italic>mt<\/jats:italic>) \/apicoplast (<jats:italic>apico<\/jats:italic>) barcode was developed to estimate genetic diversity and infer the evolutionary history of <jats:italic>Plasmodium falciparum<\/jats:italic> across the major distribution ranges. However, the <jats:italic>mt<\/jats:italic>\/<jats:italic>apico<\/jats:italic> genomes of <jats:italic>P. falciparum<\/jats:italic> isolates from the CMB region to date are poorly characterized, even though this region is highly endemic to <jats:italic>P. falciparum<\/jats:italic> malaria.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>We have sequenced the whole <jats:italic>mt\/apico<\/jats:italic> genome of 34 CMB field isolates and utilized a published data set of 147 <jats:italic>mt\/apico<\/jats:italic> genome sequences to present global genetic diversity and to revisit the evolutionary history of the CMB <jats:italic>P. falciparum<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Genetic differentiation based on <jats:italic>mt\/apico<\/jats:italic> genome of <jats:italic>P. falciparum<\/jats:italic> revealed that the CMB (Lazan, Myanmar) isolates presented high genetic diversity with several characteristics of ancestral populations and shared many of the genetic features with West Thailand (Mae Sot; WTH) and to some extent West African (Banjul, Gambia; Navrongo, Ghana; WAF) isolates. The reconstructed haplotype network displayed that the CMB and WTH <jats:italic>P. falciparum<\/jats:italic> isolates have the highest representation (five) in the five ancestral (central) haplotypes (H1, H2, H4, H7, and H8), which are comparatively older than isolates from other SEA populations as well as the WAF populations. In addition, the highest estimate of the time to the Most Recent Common Ancestor (TMRCA) of 42,400 (95% CI 18,300\u201382100) years ago was presented by the CMB <jats:italic>P. falciparum<\/jats:italic> compared to the other regional populations. The statistically significant negative values of Fu's <jats:italic>F<\/jats:italic>s with unimodal distribution in pairwise mismatch distribution curves indicate past demographic expansions in CMB <jats:italic>P. falciparum<\/jats:italic> with slow population expansion between approximately 12,500\u201320,000 ybp.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The results on the complete <jats:italic>mt\/apico<\/jats:italic> genome sequence analysis of the CMB <jats:italic>P. falciparum<\/jats:italic> indicated high genetic diversity with ancient population expansion and TMRCA, and it seems probable that <jats:italic>P. falciparum<\/jats:italic> might have existed in CMB, WTH, and WAF for a long time before being introduced into other Southeast Asian countries or regions. To reduce the impact of sample size or geographic bias on the estimate of the evolutionary timeline, future studies need to expand the range of sample collection and ensure the representativeness of samples across geographic distributions. Additionally, by mapping global patterns of <jats:italic>mt\/apico<\/jats:italic> genome polymorphism, we will gain valuable insights into the evolutionary history of <jats:italic>P. falciparum<\/jats:italic> and optimised strategies for controlling <jats:italic>P. falciparum<\/jats:italic> malaria at international borders.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s13071-024-06629-3","type":"journal-article","created":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T15:54:52Z","timestamp":1735574092000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["The evolutionary history of Plasmodium falciparum from mitochondrial and apicoplast genomes of China-Myanmar border isolates"],"prefix":"10.1186","volume":"17","author":[{"given":"Yini","family":"Tian","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Run","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongmei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yilong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,12,30]]},"reference":[{"key":"6629_CR1","unstructured":"WHO. 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