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Large subunit gene of rubisco (rbcL) of cyanobacteria Arthrospira platensis FACHB341, A. Platensis FACHB439, A. Maxima OUQDSM and Spirulina sp. FACHB440 is cloned, sequenced and characterized. Results show that GC content of the gene in strain Spirulina sp. FACHB440 is higher than that in the others. The alignments based on deduced amino acid sequences indicate that Spirulina sp. FACHB440 is different from that in other three samples of Arthrospira, though they have the same conserved functional sites (95, 98, 121, 124, 221, 257). The nucleotide sequence similarity among the three strains of the genus of Arthrospira (96.5～99.6%) is higher than that between Arthrospira and Spirulina (78.1～78.5%). By comparison of the corresponding sequence of other cyanobacteria, a phylogenetic tree with two clusters is constructed. A. Platensis FACHB341, A. Maxima OUQDSM and A. Platensis FACHB439 form the monophyletic linage, which is fully supported by bootstrap values (1000), while Spirulina sp. FACHB440 and Anabaena sp. PCC7120 cluster in another linage with the bootstrap value of 909.