In the present study, 24 cyanobacterial strains with regular helical trichomes were isolated from four different freshwater bodies in China. These strains were initially identified as a freshwater Arthrospira-like cyanobacterium. Analysis of their 16S ribosomal RNA gene sequences revealed that these strains formed a monophyletic group with Planktothrix. Further molecular phylogenetic analyses based on the cpcBA-IGS and rpoC1 genes supported the finding that these strains belonged to Planktothrix, not Arthrospira. In addition, the fatty acid composition showed that the strains contained 18:3α but lacked 18:3γ, which was similar to Planktothrix. These results showed that the alga formed a new group within Planktothrix and that this group, which resembled Arthrospira in morphology, was unrelated to Arthrospira. The strains were distinct from previously described Planktothrix species, and therefore a new species, Planktothrix spiroides sp. nov., was established.