Abstract: In order to analyze the variations of ITS sequences in Musa, the ITS sequences of 33 wild species from different geographical origin in Musa were amplified by PCR and sequenced, and then the NJ tree was constructed by ITS sequences. The results showed that, the sequences of the ITS in Musa had a strong phylogenetic signal. 108 (24.43%) informative base sites were detected. And a lot of indels and/or single base substitutions were observed in the sequences of various samples in Sect. Australimusa, which had 21 different sequence sites from other sections. According to the analysis of the sequences, we could infer that Sect. Australimusa might be the inter-specific hybrids between M. schizocarpa and M. balbisiana (ITC0271). Sect. Eumusa and Sect. Rhodochlamys had no difference in the sequences. The ITS sequence differentiation was possibly affected from the influence of the geographic distribution. A new species, M.tongbiguanensi identified by Chen, could be distinguished from other species in ITS sequence. It proved that M.tongbiguanensi might be a new species in molecular level. The sequences analysis of ITS was good to discriminate the phylogenetic relation between species/subspecies in Musa.