Fed-batch cultures of Klebsiella pneumoniae expressing Escherichia coli aldH were performed under microaerobic conditions to investigate the effects on metabolites production. Increasing the aeration rate enhanced cell growth and 3-hydroxypropionic acid (3-HP) production, but reduced 1,3-propanediol (1,3-PDO) formation. The recombinant strain K. pneumoniae/pUC18kan-aldHec produced 48.9 g/L of 3-HP and 25.3g/L of 1,3-PDO with an overall yield of 0.66 mol/mol in 28 h at an aeration rate of 1.5 vvm; however, under fully aerobic condition, no 3-HP and 1,3-PDO were produced due to the repression of dha operon. The flux through the reaction catalyzed by glycerol dehydratase and the split ratio of 1,3-PDO were negatively correlated with the aeration rate, even though the 3-HP level showed a positive trend. This study demonstrated that the relative amounts of 3-HP and 1,3-PDO can be controlled by the aeration rate.