Macleaya cordata, in the Papaveraceae family, is a common medicinal plant used for benzylisoquinoline alkaloids and other alkaloids. Current research into M. cordata has focused on the composition, bioactivity and pharmacology of alkaloids. The anatomical structure of M. cordata organs and histochemical localization of alkaloids, closely related to alkaloid synthesis, transport and storage, have not been reported. Here we show the morphologic characters of greenhouse-grown M. cordata plants and developmental anatomic structure of main vegetative organs by hand sectioning and the histochemical localization of alkaloids in roots, stems and leaves by Dragendorff reagent. M. cordata is a typical dicotyledonous plant. Abundant alkaloid accumulation occurred in parenchymal cells and cells around the vessels of stele of roots, cells near the vascular bundles of stems and petioles, and occasionally in the pith of stems. Overall, the amount of alkaloids in roots is higher than that in stems.