The Panax bipinnatifidus species complex (P. bipinnatifidus and its close relatives) in the Sino-Himalayan region has been taxonomically difficult. Evolutionary analyses using amplified fragment length polymorphism (AFLP) markers were carried out on 125 individuals representing 11 populations of the P. bipinnatifidusspecies complex and one population of P. stipuleanatus Tsai & Feng as an outgroup. The populations from the eastern Himalayan region, sampled from Nepal and eastern Tibet, formed two main groups in the neighbor-joining and split network analyses. The Pailong population (Tibet-PL) in eastern Tibet showed a highly distinct AFLP profile and was placed as the most basally branched group in the neighbor-joining tree. The remaining Himalayan populations showed three subgroups: the Nepal-HB and Nepal-HS subgroup, the Nepal HH subgroup, and the Tibet-BY subgroup. The three Himalayan subgroups had very limited gene flow among them and showed subtle morphological differences. The populations in eastern, central, and western China showed clear geographic patterns and can be sorted into several geographical groups. Each major group in the species complex has strong bootstrap support, but relationships among them are poorly resolved, which is consistent with a pattern of evolutionary radiation. The strong geographic grouping, high Nei's population differentiation index, and limited gene flow among populations in different regions support the importance of geographic isolation in the diversification of the P. bipinnatifidus species complex in the Sino-Himalayan region.