Anatoxin-a and homoanatoxin-a are neurotoxic cyanotoxins produced by benthic and planktonic cyanobacteria worldwide. These toxins are produced by the cyanobacterial genera Dolichospermum, Cuspidothrix, Phormidium, Oscillatoria, Tychonema and Cylindrospermum. In the present study the ana gene clusters (anaA-anaG; c. 21.1 kilobases) of two anatoxin producing Cuspidothrix issatschenkoi strains from Germany: (NIVA-CYA 711) and New Zealand (CAWBG02) were sequenced and compared with the ana gene clusters of two C. issatschenkoi strains from Japan (RM-6 and LBRI48) and one from China (CHABD3). All five ana gene clusters are characterized by the same gene order for anaA-anaG. Similarities were highest (99.56-99.57%) between German (NIVA-CYA 711), New Zealand (CAWBG02) and Chinese (CHABD3) strains. Similarities were lower (91.40-91.67%) when compared to the Japanese strains (RM-6 and LBRI48). Collectively, 2,037 variable sites (328 single nucleotide polymorphisms and 9 insertions/deletions, comprising 1,709 nucleotides) were found in the ana gene clusters of the German, New Zealand and Japanese strains compared to the Chinese strain (CHABD3). The ana gene clusters of the German (NIVA-CYA 711), New Zealand (CAWBG02) and Japanese (RM-6 and LBRI48) strains were characterized by 83, 84, 255 and 231 SNP's compared to the Chinese strain (CHABD3), respectively. The anaE and anaF genes showed the highest variability in all five strains and are recommended as the best genetic markers for further phylogenetic studies of the ana gene cluster from C. issatschenkoi.