Panax notoginseng is a perennial herb with long growth period and reproduction cycle. The inter-population diversity was low while the intra-population diversity among individual plants remained higher. Among them， the ginsenosides content of individual plants were significantly different among groups， providing a theoretical basis for deploying the group selection approach. In this study， 11 group populations （SL1-SL11） were constructed according to the content of five saponins （notoginsenoside R1， ginsenoside Rg1， ginsenoside Rb1， ginsenoside Re， ginsenoside Rd） in P. notoginseng. The contemporary and first generation group population were compared and analyzed base on the saponins content. In addition， the genetic diversity of populations was evaluated by using 17 pairs of polymorphic SSR markers that were identified from a total of 255239 SSR polymorphisms. Resulted from the genetic diversity of the first generation population of SL1-SL11 that were evaluated by SSR markers， the high heterozygosity （0.4583-0.6042）， low genetic differentiation （Fst=0.0447）， and high gene flow （Nm=11.6189） were observed. Although there were no significant difference in total saponin among the populations， the coefficient of variation for notoginsenoside R1 was higher than that for total content of five saponins and other monomeric saponins. The notoginsenoside R1 content in the SL8 population was significantly higher than that of other populations. Collectively， this study produced group populations using saponin content as the target trait， and evaluated their genetic diversity using SSR markers. The newly-generated population with higher notoginsenoside R1 content can serve as breeding material in breeding of Panax notoginseng.