We examined the phylogenetic assignment of the Chinese strain PCC 9901, a cyanobacterium previously identified as Lyngbya laxespiralis, using phenotypic and molecular approaches. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain PCC 9901 clustered with Arthrospira rather than Lyngbya. While all the Arthrospira strains were assigned to four genotypes (clusters IA, IB, IIA and IIB) based on the 16S-23S internal transcribed spacer (ITS) rRNA sequences, we reported here an unexpected new genotype for strain PCC 9901 that we named cluster III. A mosaic-like structure was found in two of the three intergenic spacer regions of the ITS (ISR1 and ISR3). In addition, a short repeated sequence was specific for genotype I, and a motif was found in genotype II sequences, but they were absent from the PCC 9901 ITS sequence, suggesting multiple recombination events and/or divergent evolution. Strain PCC 9901 was therefore placed into Arthrospira, and it constituted a new ITS cluster, together with other Asian strains.