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The partial sequence of the psbA gene from Cladosiphon okamuranus was amplified by PCR and their sequences were analysed. Neighbor-joining method was used to build phylogenetic trees according to the psbA sequence among 11 species, C. okamuranus included, that are affiliated to the algal order Ectocarpales. The results showed that the nucleotide sequence is 737 bp and the sequence shares high homology with identity above 96% to the psbA gene of D. foeniculaceus, M. simplex, A. fistulosus, C. flagelliformis, P. latifolia, E. sp. SMB-2004, I. sinicola, C. sinuosa, H. clathratus and P. fascia. The psbA gene is accepted by GenBank (Accession number: EU332142). 245 amino acids are deduced from 737 bp nucleotides. Analyzing the codon usage of these amino acids, we found the problem of preference of codon usage. The phylogenetic tree shows that C. okamuranus is separated from the other Chordariaceae family members such as D. foeniculaceus, C. flagelliformis, A. fistulosus and P. latifolia.