We examine phylogenetic relationships among species and populations of Asian cavity-nesting honeybees, emphasizing detection of potential unrecognized species in the geographically widespread Apis cerana Fabricius (Hymenoptera, Apidae).  We carried out a phylogenetic analysis of genome-wide single nucleotide polymorphisms (SNPs) using BEASTv1.8.4 and IQ-TREE 2. Our samples cover the largest geographic area and number of populations of Asian cavity-nesting honeybees sampled to date. Nodes in the tree were calibrated using the mid-Miocene giant honeybee Apis lithohermaea Engel. We used STRUCTURE, Bayes Factor Delimitation, and discriminant analysis of principal components to infer probable species among populations of cavity-nesting honeybees currently recognized as Apis cerana. Our results support four species within A. cerana: the yellow “plains” honeybee of India and Sri Lanka; the lineage inhabiting the oceanic Philippine islands; the Sundaland lineage found in Indonesia, Malaysia and parts of southeast Asia; and a Mainland lineage, which we provisionally consider A. cerana in a narrow sense.