One hundred bacterial strains capable of producing 1,3-PD from glycerol were isolated from soil and wastewater samples. The most efficient strain SU6, which could synthesize higher concentration of 1,3-PD and 1,3-propanediol oxidoreductase was selected and identified, based on biochemical characteristics and rRNA gene sequence analysis. The results indicated that this strain is a member of Klebsiella pneumoniae. A mathematical model was developed to investigate the influences of each medium composition and their interactions on the production of 1,3-PD and 2,3-BD under micro-aerobic and anaerobic cultivation. The maximal concentrations of 1,3-PD and 2,3-BD under micro-aerobic fermentation were higher than those under anaerobic cultivation. The maximum yield of 1,3-PD (24.98 g/l) was achieved in the medium containing 200 g/l crude glycerol (27%), 1.96 g/l yeast extract, 2.87 g/l ammonium phosphate and 2.16 g/l sodium fumarate. Under this condition, 2,3-BD production was 9.54 g/l. Verification on the medium optimization revealed the maximum 1,3-PD and 2,3-BD concentrations of 24.14 and 9.16 g/l, respectively. This resulted in significantly increase by 6.1 and 2.9 folds, respectively.