ITS2 characterization and Anopheles species identification of the subgenus Cellia

► We study the ITS2 sequence divergence, phylogeny and secondary structure of Anophelines. ► ITS2 length was variable and no intraspecific variations were found. ► Significance was found between repeats, minimum free energy and RNA secondary structures. ► Four domain types in secondary structure and unique microsatellites were identified. ► ITS2 region is more species-specific and useful for Anopheles species identification.