Honeybee is native from Africa, Europe and western Asia and its presence elsewhere in the world is due to human imports. In New Caledonia, importation of Western-Europe M lineage honeybees from France started in the 19th century and these black honeybees were dominant until the late 1980’s when an American foulbrood infestation decimated the colonies and Eastern-Europe C Lineage importation began from Australia, New Zealand and Italy. Nowadays, the hybrid honeybee is the most frequently bred but A. m. mellifera persists. The New Caledonia Islands offers the opportunity to study the genetic admixture of two human-mediated driven and temperate European subspecies into a favorable tropical landscape. Within the framework of the INRA-ITSAP SeqApiPop project, we sequenced the whole-genome of 40 honeybees sampled from Grande Terre, the largest island of the archipelago, and from 3 medium size islands (Lifou, Maré and Ouvéa). When compared with population samples from Europe including A. m. mellifera, A. m. ligustica, A. m. carnica and A. m. caucasica, the New Caledonia honeybee population indeed reveals a mixed composition of A. m. mellifera and A. m. ligustica. The honeybees from Grande Terre have a higher proportion of A. m. ligustica background whereas the honeybees from Lifou have a higher proportion of A. m. mellifera. Maré shows an intermediate profile with a higher proportion of A. m. mellifera background than Grande Terre. The Ouvéa honeybee’s background is similar to Grande Terre, and yet the Ouvéa colonies originate from a recent importation of A. m. ligustica queens. Despite a substantial importation of A. m. ligustica and the decline of the first introduced black honeybee, the genetic composition of New Caledonia honeybees is still characterized by a strong presence of an A. m. mellifera background. Our whole-genome results comfort previous studies on Lifou, suggesting this island could be considered as a black honeybee conservatory in the South Pacific Ocean.