A total of 1.1 kb including whole ITS (intertranscribed spacer), part of 5.8S rDNA and 2S rDNA were sequenced. The results reveal that D. pallidifrons, Taxon I and Taxon J share the same sequence, and D. albomicans and D. s. neonasuta have the other same one. Among the sequences, there were a handful of insertions, deletions and substitutions. Insertions and deletions occur mainly between outgroup and ingroups; yet only 1 insertion and 12 deletions were detected in D. niveifrons, and 1 deletion was found in D. s. sulfurigaster. Among all the substitutions in outgroup and ingroups, totally 55 transitions and 65 transvertions were detected. The value of transition transvertion is quite different to that of mitochondrial genome. We applied parsimony and NJ methods to reconstruct the phylogenetic relationships of the 7 taxa. They show that D. niveifrons is on the basis of the trees, which suggests that it be less related to the rest; D. albomicans, D. s. neonasuta, D. pallidifrons, Taxon I and Taxon J are more related. We suggested that more related topology of D. s. sulfurigaster and D. s. neonasuta due to the specific evolution of ITS, yet not meaning their real relationships. Sequence variations and phylogeny analysis reveal that the ITS may be not an informative marker to nasuta subgroup. However, secondary structure analysis by using PCFOLD 4.0 reveals that the structure of the ITS is quite conservative; the stem-loop of ITS 3'-end may be an important structure of rDNA splicing.