We report the genome sequence of Bifidobacterium animalis subspecies lactis BL3, which has preventive properties on acute colitis and colon cancer. The genome of BL3, which was isolated from Korean faeces, consisted of a 1 944 323 bp size single chromosome, and its G+C content was 60.5%. Genome comparison against the closest Bifidobacterium animalis strain revealed that BL3 had particularly different regions of four areas encoding flavin-nucleotide-binding protein, transposase, multidrug ABC transporter and ATP binding protein.