In this work, we investigated the molecular stable isotope compositions of hydrate-bound and dissolved gases in sediments of the Amazon deep-sea fan and adjacent continental slope, Foz do Amazonas Basin, Brazil. Some cores were obtained in places with active gas venting on the seafloor and, in one of the locations, the venting gas is probably associated with the dissociation of hydrates near the edge of their stability zone. Results of the methane stable isotopes (δ13C and δD) of hydrate-bound and dissolved gases in sediments for the Amazon fan indicated the dominant microbial origin of methane via carbon dioxide reduction, in which 13C and deuterium isotopes were highly depleted (δ13C and δD of −102.2% to −74.2% V-PDB and −190 to −150% V-SMOW, respectively). The combination of C1/(C2+C3) versus δ13C plot also suggested a biogenic origin for methane in all analysed samples (commonly >1000). However, a mixture of thermogenic and microbial gases was suggested for the hydrate-bound and dissolved gases in the continental slope adjacent to the Amazon fan, in which the combination of chemical and isotopic gas compositions in the C1/(C2+C3) versus δ13C plot were <100 in one of the recovered cores. Moreover, the δ13C-ethane of −30.0% indicates a thermogenic origin.