Objective: To depict mitochondrial genetic variation for the first time among Anopheles minimus (. An.minimus) (Diptera: Culicidae) species from two malaria endemic states of NE India. Methods: Phylogeographic analysis was carried at 9 out of 12 sites of An.minimus confirmed malaria endemic places. Results: All sequences were Adenine-Thymine rich regions. Transitions were observed in 6 sequences where 5 mutations were synonymous substitutions and in 1 case non synonymous mutation was observed. Three distinct clusters of haplotypes were generated. Haplotype diversity and low nucleotide diversity were studied. Overall negative values obtained from Tajima's D test and Fu'sF