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Background The malaria vector Anopheles minimus has been influenced by external stresses affecting the survival rate and vectorial capacity of the population. Since An. minimus habitats have continuously undergone ecological changes, this study aimed to determine the population genetic structure and the potential gene flow among the An. minimus populations in Thailand. Methods Anopheles minimus was collected from five malaria transmission areas in Thailand using Centers for Disease Control and Prevention (CDC) light traps. Seventy-nine females from those populations were used as representative samples. The partial mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and cytochrome b (Cytb) gene sequences were amplified and analyzed to identify species and determine the current population genetic structure. For the past population, we determined the population genetic structure from the 60 deposited COII sequences in GenBank of An. minimus collected from Thailand 20 years ago. Results The current populations of An. minimus were genetically divided into two lineages, A and B. Lineage A has high haplotype diversity under gene flow similar to the population in the past. Neutrality tests suggested population expansion of An. minimus, with the detection of abundant rare mutations in all populations, which tend to arise from negative selection. Conclusions This study revealed that the population genetic structure of An. minimus lineage A was similar between the past and present populations, indicating high adaptability of the species. There was substantial gene flow between the eastern and western An. minimus populations without detection of significant gene flow barriers. Graphical abstract

Additional file 1: Text S1. Supplementary methods detailing generation of the DsRedKPP strain. Text S2. Determination of high and low laboratory diet quantities via a preliminary pilot study. Figure S1. Weighted larval development and pupation rates across pilot diet treatments, plotted as a function of time (from hatch). a Mean daily instar (Âą standard error) of all remaining larvae (i.e. those which had not pupated or died). b Total number of pupae counted each day. Table S1. Wing lengths of adult males from different diet treatments (n = 12 per treatment).

Additional file 2: Table S2. Summary of experimental blocking design. Table S3. Nutritional content analyses of mosquitoes in experimental treatment groups. Figure S2. Wing lengths of adults from all larval treatments, separated by experimental block. Table S4. Full results of semi-field cage mating competition experiment.

Additional file 2: Table S2. Summary of experimental blocking design. Table S3. Nutritional content analyses of mosquitoes in experimental treatment groups. Figure S2. Wing lengths of adults from all larval treatments, separated by experimental block. Table S4. Full results of semi-field cage mating competition experiment.