The stems of Dendrobium thyrsiflorum RCHB.F. ex ANDRÉ can be processed into an important class of Traditional Chinese Medicine named "Huangcao Shihu," which has diverse curative effects, such as nourishing yin and clearing away unhealthy heat, benefiting the stomach, and promoting the production of body fluid. The identification of the geographical origin of D. thyrsiflorum is vital for preserving its natural resource and ensuring the quality of "Huangcao Shihu." In order to identify the origin of D. thyrsiflorum on Chinese herbal medicine market, 14 D. thyrsiflorum-specific microsatellite markers were developed in this study. Assignment tests were performed by the microsatellite marker analysis coupled with three new statistical approaches (partially Bayesian, frequency-based, and fully Bayesian methods) to determine the origin populations of 12 commercial samples of "Huangcao Shihu" collected from a medicine market in Nanjing, Jiangsu Province, China. Their genotypes were compared with those of 136 individuals belonging to five wild D. thyrsiflorum populations from China, Thailand, India, Myanmar, and Laos. Comparisons of the probabilities of 12 unknown individuals originating from each candidate population indicated that most of them appeared to originate from Myanmar and Laos. This suggests that the two countries may be the predominant sources of D. thyrsiflorum on the medicine market in Nanjing. In addition, the 14 microsatellite markers developed in this study may be an effective tool for identification of the origin of commercial available "Huangcao Shihu" and play an important role in its quality control.