Curculigo orchioides and Curculigo latifolia (Hypoxidaceae) have been widely used as traditional medicines in Indonesia and other Asian countries for antihyperglycemic, aphrodisiac, antioxidant, and antimicrobial treatments. This work aimed to determine the distribution of secretory structures and metabolites. Metabolite profiling approach of the plant organs was determined by UHPLC-Q-Orbitrap-HRMS. Histochemical-based techniques on rhizome, root, petiole, and leaf, with transversal sections on fresh samples, were prepared using a razor blade to determine the secretory structures of the plants, followed by plant anatomy procedures. Histochemical analysis was carried out using several reagents to detect the metabolites. Metabolite profiling revealed several classes of compounds, i.e. phenolics, alkaloids, terpenes, essential oils, and lipophilic. Secretory cavities and idioblast cells, were detected in both species and localize a diverse metabolites. Additionally to the specialized structures, hypodermis, epidermis, intercellular spaces, and cuticle also contain some of those compounds. The secretory structures spread over the different organs. This discovery may be useful to distinguish particular organs as medicine source, which does not only depend on the availability of rhizome. The secretory structures and the chemical compounds of the two species, described herein for the first time, can be used further in plant identification purposes based on chemical markers. © TÜBİTAK.