Dissolved methane (CH4) concentrations were measured in the water column at 25 stations along the four sections above Koko and Jingu guyots (the southern part of Emperor Seamount chain). The measured methane concentrations were relatively low (1–6.5 nM). The patterns of CH4 vertical distributions over Koko and Jingu were different. The greatest dissolved methane concentrations (6.5 nM) were found in the near-bottom layer (357 m) above the Koko summit. For Koko guyot, the greatest CH4 content (3.9–6.5 nM) was mainly associated with the subsurface (10–300 m) layer above the summit. However, another methane plume (6 nM) was detected at 1000 m on the western slope of the guyot. We propose that methane maximum was caused by the influence of the Kuroshio Extension or deep eddies. The CH4 distribution over Jingu gyuot was similar to that in open ocean waters. The greatest methane concentrations (3.8–6 nM) were found in the subsurface layers above the summit. Methane exceeded atmospheric equilibrium concentration in the surface (5–52 % supersaturation) layer for both Koko and Jingu. The methane content and supersaturation level in the subsurface layer was at least two times higher than previously measured values for the open ocean. We believe that the high methane and supersaturation level was caused by enhanced methanogenesis in the water column above the seamounts. The estimated methane flux to the atmosphere varied from 1.4 to 16.3 μmol m−2 day−1 for Koko and from 0.5 to 6.5 μmol m−2 day−1 for Jingu, respectively. The average fluxes calculated for Koko (8.37 μmol m−2 day−1) and Jingu (2.8 μmol m−2 day−1) were significantly greater than the average flux for open and coastal oceans. Given the substantial methane atmospheric contributions, the global methane budget should be reconsidered.