Geographic factors play an important role in the species distribution and divergence of natural populations in plants. Here we re-analyzed 14 SSR markers data in 39 populations from Fargesia spathacea complex, aimed to reveal how geographic factors may influence the pattern of genetic diversity and divergence of Fargesia spathacea complex. We found that Fargesia scabrida sub-clade exhibited the highest genetic diversity (He=0.50) while Fargesia oblique sub-clade exhibited the lowest one (He=0.33). On the level of clade A and B, genetic diversity was proved to be significantly positive correlated to altitude and latitude; but on the level of sub-clade, we detected negatively correlations between genetic diversity and altitude, latitude, which indicated that some other factors may have an impact on the genetic diversity within Fargesia spathacea complex. On the other hand, we carried out Mantel test and found that geographic distance may not be the driving force of the current genetic divergence pattern within Fargesia spathacea complex. Clade B showed no significant correlation between genetic distance and geographic distance, and only one sub-clade in clade A showed slightly significant correlation. Thus, we inferred that natural selection, gene flow and genetic drift may influence the genetic differentiation within these species. These findings provide important information for further study of giant panda’s staple food.