This paper focused on the biological characteristics of Changtai Fructus Amomi, carried out its molecular identification, and cleared its taxonomic status, which laid the foundation for the origin brand building of Changtai Fructus Amomi. According to the combining field observations and measurements of the biological characteristics of Changtai Fructus Amomi with the indoor research, this paper analyzed ITS-5.8S sequences of the different Amomum species. It indicated that there is no significant difference of Fructus Amomi flowers, leaves, fruits and other major biological indicators between Xinwu Village, Chenxiang Town and Shanchong Village, Mayangxi tourist area, Changtai County. It also showed that the percentage of fertile fruit, ripening rate, 1000-gain weight and acre yield of Xinwu Village, Chenxiang Town are significantly higher than Shanchong Village of Mayangxi tourist area. According to the Phylogenetic trees, which were constucted based on ITS-5.8S sequences, Changtai Fructus Amomi, Amomum villosum and Amomum villosum Lour.var.xanthioides T.L.Wu et Senjen clustered into a branch with the 99 percent support. The homology of Changtai Fructus Amomi and the other two kinds all reached more than 99 percent. Therefore it is found that Changtai Fructus Amomi and Amomum villosum should be the same based on the morphological characteristics and ITS-5.8S.