Abstract: Armeniaca hongpingensis C. L. Li is a narrowly distributed species, which has been hypothesized to be a natural hybrid of A. vulgaris Lam. and A. mume Sieb. based on morphological similarity. However, related molecular phylogenetic research is still lacking. In this study, the phylogenetic relationship between A. hongpingensis and other Armeniaca species was investigated using individuals and seedlings of A. hongpingensis and individuals of five other Armeniaca species (e.g., A. vulgaris, A. mume, A. mume Sieb. var. bungo Makino). Two nuclear genes (ITS and SBEI) and two chloroplast genes (matK and ycf1b) were sequenced to reconstruct molecular phylogenetic trees. matK, ycf1b, and SBEI were also used to reconstruct a haplotype network. Phylogenetic analyses of both nuclear and chloroplast genes showed that the individuals and seedlings of A. hongpingensis grouped together with high bootstrap values (99/79, 71/81), independent of other Armeniaca species. The Bayesian phylogram based on ITS sequences showed that most individual and seedling clones of A. hongpingensis were grouped into two single clades with high bootstrap values (0.82, 0.97); the other clones clustered with A. vulgaris and A. mume var. bungo individuals; and no clones clustered with A. mume individuals. On SBEI and ycf1b loci, haplotypes of A. vulgaris, A. mume, and A. holosericea were not detected in A. hongpingensis; whereas on the matK locus, only haplotypes of A. vulgaris were detected in a few (2/9) seedlings of A. hongpingensis. These results suggest that A. hongpingensis is likely an independent species rather than a natural hybrid of A. vulgaris and A. mume, with a closer genetic relationship as well as detectable gene flow with A. vulgaris.