Klebsiella pneumoniae strain ATCC 25955 is a 1,3-propanediol-producing bacterium that is insensitive to oxygen. Here, we present a 5.29-Mb assembly of its genome sequence. We have annotated 10 coding sequences (CDSs) for 1,3-propanediol fermentation and 18 CDSs for glycerol uptake. The CDSs related to virulence and by-product formation were also annotated.