“Headspace” technique is one of the methods for the onboard measurement of hydrogen (H2) and methane (CH4) in deep seawater. Based on the principle of an automatic headspace commercial sampler, a specific device has been developed to automatically inject gas samples from 300 ml syringes (gas phase in equilibrium with seawater). As valves, micro pump, oven and detector are independent, a gas chromatograph is not necessary allowing a reduction of the weight and dimensions of the analytical system. The different steps from seawater sampling to gas injection are described. Accuracy of the method is checked by a comparison with the “purge and trap” technique. The detection limit is estimated to 0.3 nM for hydrogen and 0.1 nM for methane which is close to the background value in deep seawater. It is also shown that this system can be used to analyze other gases such as Nitrogen (N2), carbon monoxide (CO), carbon dioxide (CO2) and light hydrocarbons.