This study presents the genome sequence of Synechococcus sp. strain C9 (= CCMEE 5213 = ATCC 700244), a thermophilic unicellular cyanobacterium that was originally isolated from a thermal pool at Octopus Spring, Yellowstone National Park, USA. The genome consists of a 2,958,309-bp chromosome with a GC content of 52.9% and 2,854 protein-coding sequences.