Zanthoxylum genus (Rutaceae) comprises about 212 species distributed in warm temperature and subtropical areas in the worldwide. Zanthoxylum species have been used in traditional for the treatment of tooth decay, snakebites, blood circulation problems, stomach problems, inflammation, rheumatic, and parasitic diseases. The chemical investigations of Zanthoxylum have been studied by many scientists over the world. Several classes of compounds have been isolated from this genus such as alkaloids, coumarins, and monoterpenes. Of these, alkaloids are the main components and play an important role in Zanthoxylum species. Alkaloids have been shown the potential promise about biological activities: cytotoxic, antimalarial, leishmanicidal, anti-inflammatory, analgesic, antiviral, and antibacterial activities. This chapter will focus on the structure elucidation and pharmacological activities of alkaloids from Zanthoxylum species. In addition, the absolute configuration of some alkaloids from Zanthoxylum genus will be also discussed.