Difficulties in phylogenetic reconstruction are common within the woody bamboos due to their unique life cycles, a lack of morphological characters and even an absence of molecular evidence. The genetic variability and population structure of the bamboos are also poorly understood which impedes their exploitation via breeding. In this paper, ITS sequence data were used to examine the degree of genetic variation within the alpine bamboos and to explore their phylogeny. Twenty-three species representing three genera, Thamnocalamus, Fargesia and Yushania, of the alpine bamboos and one species of Ampelocalamus as an outgroup were studied. The results indicated that Thamnocalamus spathiflorus var. crassinodus and the Fargesia spathacea clade form the basal groups but bootstrap support was weak. Among the rest of the species, including species previously placed in Fargesia (plus Borinda) and Yushania, the F. yunnanensis subclade and the F. communis subclade were recognized but internal support for such groups was again low. The result indicated that, Fargesia and Yushania as delimited by morphological characters, are not monophyletic in the ITS phylogeny and require further resolution. We revealed relatively high levels of genetic variability in the alpine bamboos and showed that the ITS region could be used to improve generic delimitation of the woody bamboos in general.