Survey for Drosophila was carried out in Lumami (which is a hamlet in Zunheboto district of Nagaland and is head quarters of the Nagaland University) and Drosophila hegdii was one among the 16 species collected. Based on the morphological markers, internal characters a new species, Drosophila hegdii, was identified. Drosophila hegdii resembles Drosophila vulcana and Drosophila jambulina in certain morphological markers, but differed with them in multiple morphological markers. It also differs from other known species of montium sub group in characters such as the number of teeth in sex comb, and abdominal banding pattern. In order to confirm new species status with the aid of molecular markers and decipher molecular phylogeny we took advantage of “DNA Barcoding” by analysing sequences of mitochondrial cytochrome c oxidase subunit I (COI) (its 648 base pair fragment is the standard marker for “species identification” in the Barcode of Life Project). Neighbour joining trees were constructed using MEGA5 (Neighbor-Joining Tree (NJ) method with bootstrap test-1000 replicates) using the Kimura 2-parameter model, with gaps treated by pairwise deletion. Molecular phylogeny confirms the observations made with the help of morphological markers that Drosophila hegdii is a new species and closer to Drosophila vulcana and Drosophila jambulina.