In this study, the telomeres of Streptomyces cattleya DSM46488, S. mobaraensis DSM40847 and S. davawensis JCM4913 were cloned and sequenced by using self-ligation-PCR method. High sequence similarity, especially within the first 60 nucleotides(identity>80%), was revealed by the sequence alignment. At the secondary structural level, these telomeres contained multiple palindromic sequences, including the same palindromic sequences I and II. However, super-hairpin structure could not be formed by folding back of palindrome I with the internal palindromes. Moreover, the three new telomeres cloned from S. cattleya DSM46488, S. mobaraensis DSM40847 and S. davawensis JCM4913 showed sequence similarity to telomeres of linear plasmid pSHJG1 and S. albus J1074 chromosome. Phylogenetic analysis based on the first 100 nucleotides of telomeres demonstrated that they were in different phylogenetic branches from the typical telomeres and other atypical telomeres. In addition, these strains encoded the homologous putative terminal proteins-telomere associated proteins, indicating that the class of homologous atypical telomere system was widely distributed within Streptomyces.