According to scientists, there are six species of honeybees in Vietnam (five native species, an invasive species), in the six species, only two species were breeding industrialization. Pham Hong Thai (2008) and Radloff et al. (2010) showed that Vietnamese native species have two species they are Apis cerana indica Fabricius 1798 and Apis cerana cerana F. 1793. This species are very diverse in both genetic and morphological. For understanding the biodiversity of domestic honeybees at Thai Nguyen to support for other studies, bee worker in Dong Hy, Dai Tu, Phu Luong districts were collected, compared with standard samples of Apis cerana indica, Apis cerana cerana and Apis dorata with 12 targets tracking of morphological and analysis based on COI gene fragments in comparison with homologous sequencesn available in the Gen Bank. Results of morphological analysis show that: Honeybees at Thai Nguyen are the same with Apis cerana indica and different to Apis cerana cerana. The COI gene sequences of the honeybee samples in Thai Nguyen are similarity of DNA sequences of Apis cerana indica with from 99.60 to 99.80 percent. Thus the native bee in Thai Nguyen belongs to Apis cerana indica.