Macro- and microscopic techniques have long been used to describe plant materials and establish plant structural profiles. These techniques are commonly used in botanical authentication to identify the genuine and closely allied species used in botanical research. Advanced microscopic techniques were used in this study to differentiate three different Piper species used as kava or kava-kava. The genuine species is Piper methysticum and the other two species commonly called false-kava or kava-kava, are Piper auritum and Piper excelsum. Macroscopic characteristics, including a black-spotted stem and fibrous root, are characteristic of P. methysticum, whereas the stem of P. auritum is greenish with no spots, and the P. excelsum stem is purple-pink. Microscopic attributes include the characteristic collenchyma of stems and the pattern of arrangement of peripheral and medullary vascular bundles. The starch grains are smaller in P. excelsum than in the other two species. Energy-dispersive X-ray spectroscopy analysis of the crystals indicates the expected calcium, magnesium, and silica, along with lesser amounts of sodium, and potassium. The crystals present in the Piper species vary in shape, size, and elemental composition. Combining macro- and microscopical techniques and resulting characteristics are instrumental in differentiating the three Piper species.