These files are COI sequences for three Anopheles species, An. pseudowillmori, An. jeyporiensis and An. maculatus.The DNA sequence alignments were used for generating FST statistics in the software Arlequin v3. Each fasta file contains sequences from two different populations, i.e. from two study sites Nonglang and Nartiang in Meghalaya. For more information please refer to the paper https://doi.org/10.1016/j.meegid.2023.105450