Cinnamomum philippinense (Merr.) Chang (Lauraceae) had been treated as the member of the genus Machilus or Persea. In this study, segments PetD~PetB, TrnV~TrnM and TrnS~TrnT of chloroplast DNA were used to analyze the relationship of C. philippinense with the species of the genera Cinnamomum, Machilus and Persea in an attempt to resolve its taxonomic status. At the same time, the relationship between genera Machilus and Persea was also discussed. The result of chloroplast DNA analysis indicated that C. philippinense was closer to Machilus than to Cinnamomum. There was no difference between C. philippinense, Machilus thunbergii, M. japonica and M. zuihoensis in 31 variable sites from 3 sequenced fragments observed. However, there were 15 sites or indels differences between the species with the genus Cinnamomum. The genetic distance between C. philippinense and Machilus spp. was 0, whereas, 0.006 between the species and C. camphora, and 0.004 compared to Persea americana. Both cluster trees of NJ and MP analyses clearly revealed three groups of the materials analyzed: one group included Cinnamomum camphora, C. subavenium; another Cinnamomum philippinense, Machilus thunbergii, M. japonica and M. zuihoensis; and the third Persea americana. From the above results and carefully comparing the morphology of the related species, we highly recommend C. philippinense to be treated under the genus Machilus. Furthermore, based on the differences in chloplast DNA, as well as cluster analysis, Machilus and Persea could not be treated as the same genus.