ABSTRACTHere, we report the complete genome sequence ofBurkholderiasp. strain FERM BP-3421, a bacterium isolated previously from a soil sample in Japan. Strain FERM BP-3421 produces spliceostatins, which are splicing modulatory antitumor agents that advanced to preclinical development. The genome is composed of four circular replicons of 3.90, 3.0, 0.59, and 0.24 Mbp.