The genus Alpinia is the largest member of Zingiberaceae, but its phylogeny is still unclear. The studies in Vietnam have been focusing only on new records and new species of Alpinia for the Vietnamese flora. Thus, an overview of the phylogeny of Vietnamese Alpinia is necessary. This work based on molecular data from matK and ITS regions of 149 species confirms that Alpinia is supported to be a polyphyletic group with six different clades. 25/37 Vietnamese Alpinia species were included in the molecular analyses, results indicated that Vietnamese Alpinia formed non-monophyletic group and was placed in clades II, IV and V of Alpinia. Most Vietnamese Alpinia are placed in clade IV, which also included species from Southern China, and South East Asia. Based on the molecular analyses, Vietnamese Alpinia is genetically closely related even though they are distributed in the whole of Vietnam including subtropical and tropical regions and their morphological apomorphies are difficult to find.