Here, we report the draft genome sequence of Epilithonimonas sp. FP211-J200, isolated from rainbow trout head kidney cells. The size of the genome is 4,110,772 bp, with a G+C content of 37.1%. The Epilithonimonas sp. FP211-J200 genome has genes related to tetracycline and β-lactam resistance. This is the first reported Epilithonimonas species genome isolated from a fish host.