The taxonomy in woody bamboo faces a lot of difficulties due to its long blooming intervals and complicated morphological variation. Whether the current taxonomy would reflect the genuine species divergence within woody bamboo is an intriguing question. Fargesia spathacea complex comprises fifteen closely related species with sympatric distribution in China. Their classification has long been controversy because of only a handful of vegetative traits available, thus providing a good opportunity to explore the evolutionary relationship and genetic differentiation in woody bamboo. Here we presented a study with 750 individuals from 39 representative populations in Fargesia spathacea complex using 14 SSR markers. We found varying degrees of genetic diversity across populations of the Fargesia spathacea complex (He=0.07-0.81) and largely negative F values at the population level, implying an excess of heterozygotes in the populations. Phylogenetic analyses revealed that all populations were divided into two major groups (cluster A and B), with the majority of fifteen species representing distinct genetic lineages. Based on the population genetic analysis along with morphological evidence, we confirmed the identity of three species (F. decurvata, F. spathacea and F. murielae) and suggested invalidation of four other species (scabrida, F. robusta, F. denudata and F. nitida). The delimitation of the rest eight species was yet to be explored. The ecological factor and spatial autocorrelation analysis supported that altitude difference might account for the distinct genetic divergence between two major groups.