Honey DNA metabarcoding provides information of floral sources of honey and foraging plant preferences of honey bees. We evaluated the floral composition of honey from two different species of honey bees, Apis cerana (ACH) and A. mellifera (AMH) in a mixed apiary located in a semi-forest environment to understand the floral preference and level of interspecific competition on floral resource. In total, 56 plant taxa were identified across the honey samples and among them, 38 taxonomic units were found in ACH compared with a total of 33 in AMH. 23 taxonomic units were found exclusively in ACH, 18 taxonomic units were found only in AMH and 15 taxonomic units were shared between ACH and AMH indicating that 73% of the taxonomic units were present only in one type of honey. The number of major plants (>1% of reads) in the honey samples was 9 and 11 in ACH and AMH, respectively, indicating a slightly higher diversity of plant taxa in AMH. Qualitative and quantitative analyses of the shared major plants revealed the division of floral resource between these co-existing honey bee species pointing to a low level of interspecific competition. We conclude that the presence of both species in the same apiary can lead honey bees to behavioral modifications to avoid competition for floral resources and to provide pollination services to a higher number of flowering plants.