Abstract: The anatomical method and histochemical method were used to study the anatomy of root and stem in Fagopyrum megaspartanium and study the distribution of flavonoids，in order to provide excellent reserves for the accumulation of effective components in F. megaspartanium. The results show that the primary xylems are tetrarch. Pith tissue is developed. The vessel of primary xylem is annular thickening and the vessel of secondary xylem is reticulate or pitted thickening. The periderm and secondary phloem contains a small amount of crystal. The secondary vascular tissues are well developed. Stems are composed of epidermis，cortex and pith. The secondary xylem and phloem fiber are developed. In root，flavonoids mainly distribute in the periderm，phloem，vascular cambium；In stem，they mainly distribute in the epiderm，collenchyma，cortical parenchyma，phloem，fascicular cambium， interfascicular cambium and xylem parenchyma. The special structure of root and stem in F. megaspartanium，can help to adapt to the arid environment. The color area of flavonoids in stem is larger than that in root.