The ice-nucleating bacterium Pantoea agglomerans (Erwinia herbicola) IFO12686 (INA+) responds to a decrease in temperature by the induction of proteins. The pattern of protein bands from strain IFO12686 following a shift in temperature from 30 to 12°C could be divided into four major groups: (1) increasing protein bands, (2) decreasing protein bands, (3) increasing–decreasing protein bands, and (4) almost constant protein bands. We identified a cryoprotective function in the increasing protein band found in strain IFO12686. The increasing protein bands that followed a reduction in temperature were considered to have an important role in cold acclimation or adaptation. We showed that these proteins possessed cryoprotective activity when tested against the freeze-labile enzyme lactate dehydrogenase. The strain IFO12686 had greater cryotolerance than Pa. agglomerans IAM1595 (INA−), and the degree of cryotolerance was increased by cold acclimation.