Alpinia officinarum Hance, which is a species of the family Zingiberaceae, is a perennial medicinal plant that is mainly distributed in the tropical and subtropical regions of Southeast Asia. Although the endophytic communities of various crop plants and several medicinal plants have been investigated, no publications have reported research related to the endophytes of A. officinarum Hance. In the present study, a culture-dependent method combined with a terminal-restriction fragment length polymorphism (T-RFLP) technique-based culture-independent method were applied to assess the diversity of the culturable bacterial endophyte communities and total bacterial endophyte communities of A. officinarum Hance. Using the culture-dependent isolation method, 136 bacterial isolates were obtained from the internal tissues of root, rhizome, stem, and leaf of healthy, 4-year-old A. officinarum Hance plants collected from Longtang Town in Xuwen County, Guangdong Province, China. We selected the A. officinarum Hance plants growing in this area because the quality and pharmacological effects of these medicinal plants growing in this area are traditionally considered to be significantly higher than those of any other areas of China. Based on 16S rDNA sequence analysis, the bacterial isolates represented 16 distinct 16S rDNA gene types, 12 distinct bacterial genera, and 15 distinct bacterial species. The most dominant bacterial population was the genus Bacillus, followed by Methylobacterium. The culturable bacterial communities that were obtained from the different tissues of the medicinal plant were significantly different, and several bacterial populations displayed some level of tissue preference in the host plant. Using the T-RFLP-based culture-independent method, 36 distinct Terminal-Restriction Fragments (T-RFs) were detected from the amplified, HhaI mono-digestion-targeted 16S rDNA gene sequences from internal tissues of the root, rhizome, stem, and leaf of A. officinarum Hance plants collected from the same sites. The corresponding taxons of the dominant T-RFs were linked to highly resistant Bacillus and Methylobacterium, as well as several marine bacterial orders, such as Oceanospirillales, Pseudomonadales, Vibrionales, and Rhodobacterales, which indicated that the population composition of the total bacterial endophyte community in A. officinarum Hance was significantly correlated with the environment of the host. The numbers of total T-RFs, the dominant T-RFs, and their corresponding taxons were significantly different between tissues of A. officinarum Hance. These observations indicated that the tissue types of A. Officinarum Hance could contribute to the variation in the bacterial endophyte communities of the plant. Furthermore, the isolated bacterial endophytes were screened for a panel of beneficial effects that included the production of extracellular chitinase and β-glucanase, indoleacetic acid (IAA), as well as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. Many of the strains displayed positive results in these assays (chitinases: 36.36%, β-glucanase: 51.52%, IAA: 54.55%, ACC deaminase: 27.27%). In particular, the isolates L-2, which was assigned to the Pantone sp., and S-16, which was assigned to the Bacillus sp., were capable of co-producing chitinases, β-glucanase, IAA, and ACC deaminase, and are potential candidates for use as biocontrol agents and in biofertilizers. In addition, two isolates (R-1, R-3) that were assigned to Rhizobium tropici could produce IAA and ACC deaminase; therefore, they are good candidates for use as plant growth-promoting bacteria.