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Here we report the complete, closed genome of the non-toxic Microcystis aeruginosa PCC7806 ΔmcyB mutant strain. This genome is 5,103,923 bp long, with a GC content of 42.07%. Compared to the published wild-type genome (Microcystis aeruginosa PCC7806SL), there is evidence of accumulated mutations beyond the inserted chloramphenicol resistance marker.