Widely distributed bottom simulating reflectors (BSRs) imply the potential existence of gas hydrates offshore southwestern Taiwan. To compare the distribution of methane concentrations along passive and active margins in the region, bottom waters and cored sediments were collected during four cruises from 2005 to 2006. The results reveal that sites with high methane concentrations are predominantly distributed in the active margin and site GS5 is the only site that contains very high methane concentrations in the passive margin of studied area. Anomalously high methane fluxes still can be obtained from the calculation of diffusive methane flux, although there might be some gas leakage during or after sampling procedures. The profiles of methane and sulfate concentration reveal very shallow depths of the sulfate-methane interface (SMI) at some sites. There is evidence that sulfate reduction is mainly driven by the process of anaerobic methane oxidation. Thus, sulfate fluxes can be used as a proxy for methane fluxes through the use of diffusion equations; and the results show that the fluxes are very high in offshore southwestern Taiwan. The depths of the SMI are different at sites GH6 and C; however, both methane profiles reveal parallel methane gradients below the SMI. This might be because of methane migration to surface sediments from the same reservoir with the same diffusion rates. Although BSRs are widely distributed both in the active margin and in the passive margin, most sites with high methane concentrations have been found in the active margin. Therefore, the specific tectonic settings in offshore SW Taiwan might strongly control the stability of gas hydrates, and thus affect the methane concentrations and fluxes of the sediments and sea waters. Furthermore, the carbon isotopic composition of methane shows that a biogenic gas source is dominant at shallower depth; however, some thermogenic gases might be introduced through the fracture/fault zones from deeper source in the active region of studied area.