Early diagenetic carbonates are rare in Lake Baikal. Siderite (Fe carbonate) concretions in the sediments were discovered only recently. Here, we discuss the first finding of rhodochrosite concretions (Mn carbonate) discovered in the near-bottom sediments of the gas hydrate-bearing seepage structure St. Petersburg-2 in the deep water environment of the Central Baikal Basin. The crystal lattice of rhodochrosite contains iron and calcium substituting to manganese. Based on pore water geochemistry and of δ ¹³C values of rhodochrosite (− 23.3 and − 29.4‰), carbon dioxide (+ 3.8 to − 16.1‰) and methane (− 63.2 to − 67.8‰), we show that carbonate crystallization most likely occurred during microbial anaerobic oxidation of organic matter, and that part of the oxygen making up the rhodochrosite seems to be derived from the ¹⁸O-rich water released from dissociating gas hydrates.