In order to explore the correlations of the histological locations and contents of the anthocyanins and saponins of the greenpurple transitional aerial stems of Panax notoginseng, we studied the histological locations of the anthocyanins and saponins of the stem parts of the greenpurple transitional aerial stems of the oneyearold P. notoginseng plants cultivated in Wenshan Prefecture, Yunnan Province by using microscopic histochemical methods.We also determined the total anthocyanin contents (TACs) and total saponin contents (TSCs) of the stem parts by using spectrophotometry, and the saponin monomer contents of the stem parts by using high performance liquid chromatogram (HPLC). The results indicated that: (1) at the middle crosssections of the stem parts, the anthocyanins were located in the 2 or 2~3 cell layers outside the cortex parenchyma and the saponins mainly in the vascular bundles. (2) The main saponin monomers of the stem parts were all Ginsenoside Rb₁. Overall, from the tips to the basal parts of the stems, the TACs, TSCs and Rb₁ contents of the stem parts displayed a “singlepeaked”, “Vshaped” and “decreaseincreasedecrease threestaged” curves, respectively. The anthocyanins accumulated mainly at the middle and superior parts of the stems, the saponins at the lower and basal parts and the Rb₁ at the superior half parts. The stem parts with the highest TAC or the lowest TSC and Rb₁ contents were just located at the golden section point of the middle and superior parts of the stems. (3) The difference among the TACs of different stem parts only reached significant level, that among the Rb₁ contents reached extremely significant level, whereas that among the TSCs did not reach significant level. For different stem parts, there were different correlation characteristics between the TAC and TSC or Rb₁ contents. For the whole aerial stems, the TAC was negatively correlated with the TSC at extremely significant level, whereas the positive correlation between the TSC and Rb₁ contents did not reach the significant level. Thus, in the greenpurple transitional aerial stems of P. notoginseng, the transversal histological locations of the anthocyanins and saponins are different and, overall and lengthways, the contents of the two compounds display negative correlation. This study could provide a reference for the exploration of the accumulation correlations of the anthocyanins and saponins of the vegetative organs of P. notoginseng.