This is the first contribution about the histochemistry of vegetative and reproductive aerial organs in the genus Piper L. Piper malgassicum accumulates alkaloids and terpenes in the epidermis and the underlying layers of parenchyma, both in the leaves, in the stems and in anthers. Some idioblasts appear to contain a large amount of secondary metabolites. The micro-anatomical analysis showed peculiar secretory structures both in the leaves, in the anthers and in the ovary. Several lipid aggregates, alkaloid droplets and calcium oxalate crystals were observed in leaves and stems, indicating their role in defence strategies, mechanical support, and pollinators attraction. In the anthers, we observed elaioplasts whose content suggest an alternative and indirect function in pollination and defence against micro-organisms. Besides, some lipid aggregates surrounded by microtubules, detected in the anthers, were recognized as lipotubuloids. The tapetum was of secretory type. Alkaloids and terpenes were widely distributed in the plant confirming the important biological role of this type of biomolecules and its functional range. In the anthers, terpene and polyphenol inclusions appeared particularly abundant in the epidermal layer, whereas calcium oxalate crystals were observed close to the ovule in the ovary at maturity.