The extensive morphological variation and broad distribution of Dendrobium species often hinder accurate identification, leading to potential misapplication and supply challenges in medicinal use. This study aimed to investigate the correlation between phytochemical composition and DNA barcoding markers based on ITS and matK to improve identification in twenty-one medicinal Dendrobium species. Phytochemical data compiled from databases were analyzed through hierarchical clustering to construct a chemical dendrogram. Seven chemical clusters were identified, characterized by key structural compounds such as bisbibenzyls, fluorenones, flavonols, phenanthrenes, and 9,10-dihydrophenanthrenes. Each chemical cluster revealed characteristic profiles of major and minor compounds among Dendrobium species. The ITS-based phylogenetic tree proved more reliable than matK for distinguishing Dendrobium sections. Correlation analysis between the phytochemical dendrogram and the ITS-based phylogenetic tree using the Fowlkes–Mallows Index (FMI) yielded a value of 0.5536, reflecting a noteworthy correlation that highlights the underlying relationship between chemical and genetic clustering. A strong correlation was observed when a phylogenetic clade contained a single chemical cluster. This pattern was evident in clades E and F, which were associated with chemical cluster 7. Cluster 7 comprised eight species, representing the largest group among all clusters. This integrative approach provides a framework for chemical forecasting and supports the authentication and sustainable utilization of Dendrobium resources in traditional medicine.