Two potentially different species of giant honey bees (subgenus Megapis) are endemic to India: Apis dorsata, the widespread low elevation form, and Apis laboriosa of the Pan-Himalayan region. Although they differ morphologically, behaviorally, and genetically, the species status of A. laboriosa remains unresolved. We sampled bees in three widely separated regions of Arunachal Pradesh, North East India, where these two taxa occurred sympatrically. We measured morphological characters of worker bees and conducted principal component analyses of two data sets (size-independent traits and the full set of characters excluding ratios). We also sequenced approximately 500 bp of the mtDNA cytochrome c oxidase subunit I (COI) and generated a phylogenetic tree. In all analyses, A. dorsata and A. laboriosa separated into well-defined groups, and with no bees showing traits suggestive of hybridization, regardless of where the species were collected. The a priori identifications of all specimens based on thoracic hair and abdominal color were verified by the analyses. Our results confirm that A. laboriosa is a valid species.