Objective:To compare the sequence difference of the ribosomal DNA second internal transcribed spacer (ITS2) in the different strains of Anopheles minimus in Yunnan. Methods: The PCR amplified rDNA ITS2 sequences, to compare the variation of An. minimus . Results: The different strains of 6 populations were sequenced, which could be separate into Anopheles minimus A and C. Conclusion: The sequence difference of the rDNA ITS2 would be very useful for the developing a molecular approach to distinguish An. minimus A and C.