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The use of medicinal plants to overcome diseases has been used since ancient times because in these plants contain secondary metabolites which can be used as medicine. The aim of this research is to observe the anatomical structure or form and the secretory cell density of secondary metabolite compound in the form of bioactive compounds. The sample used are Chromolaena odorata, Anredera cordifolia, Adenanthera pavonina, Vernonia amygdalina, Psidium guajava, Syzygium polyanthum, Piper ornatum, Zingiber officinale, dan Curcuma longa. Observation of anatomical structure of leaves was done by making paradermal and transversal sections, while observation of anatomical structure of rhizomes were performed by making transversal sections. Observations consisting of leaf anatomical structure of cells of the epidermis, the stomata and the secretory cells per unit area in the leaf and rhizome of nine tropical medicinal plants. The medicinal plants containing some of the secondary metabolite compounds. Microscopic observation found several types of secretory structure in leaves and rhizomes observed oil cavity cells were found in Syzygium polyanthum leaves, Psidium guajava leaves, Piper ornatum leaves, Anredera cordifolia leaves, and Zingiber officinale rhizomes. In Zingiber officinale and Curcuma longa rhizomes, they were found the idioblast cells which contained starch grains. In addition, there were found another form of secretory cells in Chromolaena odorata, Adenanthera pavonina, and Vernonia amygdalina. In epidermal cell, it showed the anatomy of stomata type from the leaf of medicinal plant are anomocytic stomata type, tertracytic type and cyclocytic type.