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Background  Mexico advanced to the pre-elimination phase in 2009 due to a significant reduction in malaria cases, and since 2000,  Plasmodium vivax  is the only species transmitted. During the last two decades, malaria transmission has been mostly local and isolated to a few regions. It is important to gain further insights into the impact of control measures on the parasite population structure. Hence, the aim of the current study was to determine detailed changes in  P. vivax  genetic diversity and population structure based on analysing the gene that encodes the apical membrane antigen 1 ( pvama1 ). This analysis covered from control to pre-elimination (1993–2011) in a hypo-endemic region in southern Mexico.    Results  The 213  pvama1    I-II   sequences presently analysed were grouped into six periods of three years each. They showed low genetic diversity, with 15 haplotypes resolved. Among the DNA sequences, there was a gradual decrease in genetic diversity, the number of mixed genotype infections and the intensity of positive selection, in agreement with the parallel decline in malaria cases. At the same time, linkage disequilibrium (R 2 ) increased. The three-dimensional haplotype network revealed that  pvama1    I-II   haplotypes were separated by 1–11 mutational steps, and between one another by 0–3 unsampled haplotypes. In the temporal network, seven haplotypes were detected in at least two of the six-time layers, and only four distinct haplotypes were evidenced in the pre-elimination phase. Structure analysis indicated that three subpopulations fluctuated over time. Only 8.5% of the samples had mixed ancestry. In the pre-elimination phase, subpopulation P1 was drastically reduced, and the admixture was absent.    Conclusions  The results suggest that  P. vivax  in southern Mexico evolved based on local adaptation into three “pseudoclonal” subpopulations that diversified at the regional level and persisted over time, although with varying frequency. Control measures and climate events influenced the number of malaria cases and the genetic structure. The sharp decrease in parasite diversity and other related genetic parameters during the pre-elimination phase suggests that malaria elimination is possible in the near future. These results are useful for epidemiological surveillance.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-017-2156-y) contains supplementary material, which is available to authorized users.

Temporal genetic changes in Plasmodium vivax apical membrane antigen 1 over 19 years of transmission in southern Mexico