Carbonate concretions associated with recently discovered gas hydrates from the East Sea (Sea of Japan), Korea, were investigated to delineate their origin based on textural, mineralogical and stable isotopic data. Authigenic carbonates were sampled from the 8 m-long piston core recovered from a water depth of 2072 m during a gas hydrate exploration cruise in June 2007. The carbonate concretions occur at three intervals from a depth of 220 to 280 cm from the top of core within hemipelagic muds above massive and vein-filling gas hydrate layers from depth of 329 to 655 cm. Semi-lithified carbonates occur as concretions with knobby, rounded and irregular morphologies. Textural observation of the concretions reveals porous surfaces with a spongy texture and distinctive internal layering. These concretions are mostly composed of aragonite with relatively minor contribution of calcite, with transition from calcite- to aragonite-dominating phase towards the periphery. Highly negative δ13C values (δ13C=−43 to − 27‰ PDB) suggest that methane was the main carbon source for their formation. Oxygen isotope values (δ18O = 1.1 to 3.1‰ PDB) are slightly enriched due to the relatively stable cold temperature of the East Sea bottom water (0–4 °C). Distinctively separate and narrow ranges of stable isotope compositions from each concretion and the enrichment of carbon isotopes with depth indicate that the concretions at three intervals formed independently during different periods, but under similar anoxic diagenetic conditions by anaerobic oxidation of methane. In addition, distinctive geochemical clusters of each concretion with depleting oxygen isotope trend toward the periphery strongly suggest that the concretions in this study were formed separately by pore water interactions with adjacent surrounding pelagic muds.