An air-segmented continuous-flow method has been developed for the determination of molybdenum at ultra trace levels using the catalytic effect of molybdate during the oxidation of L-ascorbic acid by hydrogen peroxide. Incorporation of an on-line ion exchange column improved the tolerance limit for various ions. The detection limits with and without the column were 64 pmol L−1 and 17 pmol L−1, and the reproducibilities at 10 nmol L−1 were 2.1% and 0.2%, respectively. The proposed method was applied to the determination of molybdenum in seawater and lake water as well as in rock and sediment samples. This method has the highest sensitivity among the available literature to our knowledge, and is also convenient for routine analysis of molybdenum in various natural samples.