Anopheles (Cellia) philippinensis Ludlow and Anopheles (Cellia) nivipes (Theobald) are two closely related, morphologically very similar, mosquito species in the Annularis group, which play a supportive role in malaria transmission in north-east India. We amplified and performed sequence analysis for the internal transcribed spacer 2 (ITS2) locus of ribosomal DNA (rDNA) gene of morphologically confirmed specimens of these two species from the states of Assam and Nagaland. An. philippinensis and An. nivipes shared 85.2% sequence similarity and no intra-species variation was found in the nucleotide sequences of the two species. Overall, sequence data of the ITS2 marker revealed that both these species from north-east India differed by as much as have been reported from specimens of eastern Thailand.