Abstract: Objective To sequence the internal transcribed spacer (ITS) regions of 28 Cryptococcus strains isolated from pigeon dropping samples and construct phylogenetic trees of 28 Cryptococcus strains and 6 Cryptococcus neoformans strains according the ITS sequences. Methods The phylogenetic trees were constructed by using neighbor-joining method and maximum parsimony method to analyze phylogenetic relationships among them and 6 references of Cryptococcus neoformans. Results All Cryptococcus strains were clustered into 3 branches, and 6 Cryptococcus neoformans strains and 6 reference strains were clustered in 1 branch. Except HP6, all HP strains and XSQ46-1 and XSQ59-3 were clustered into the same branch. Together with HP6, the DHP and XSQ strains were clustered together. According to the length of the branchs, there were no obvious differences among three main branches. Conclusion The Cryptococcus neoformans was clustered as an independent branch, however, the rest Cryptococcus species dispersed in other two branches, that is the heterogeneity of Cryptococcus genus as reported by others.