The distribution and concentration of hydrolyzable amino acids and acid-extractable free amino acids in seafloor sediments collected from the Izena and Yoron Cauldrons hydrothermal systems, Okinawa Trough, were determined. The total hydrolyzable amino acid (THAA) concentrations were between 2.95 and 20.58 μmol/g, and Gly was the most abundant amino acid, followed by Asp, Ser, Ala, Val, and Phe. The high concentration of Gly suggests that the samples were hydrothermally altered. Small amounts of D-Asp, D-Glu and D-Ala were observed in the hydrolyzable fraction of sediments. The D/L ratios were <0.15, indicating that the amino acids were biogenic. Thus, it was inferred that the source of the amino acids in the Okinawa Trough hydrothermal field is mainly bio-debris of marine planktons, such as radiolarians and foraminifera, which were observed using a scanning electron microscope with energy-dispersive spectroscopy. The acid-extractable free amino acid concentrations were between 8.56 and 104.33 nmol/g and accounted for 0.1–1.1% of the THAA. The content of free basic amino acids was much less than that of acidic and neutral amino acids, indicating that the amino acids were adsorbed on organic functional groups coating the mineral surfaces via chemical bonds. Amino acids are unstable and they rapidly decompose under hydrothermal conditions. However, the stability and survival of amino acids is enhanced via adsorption on minerals and sediment particles. Adsorption plays a role in controlling the distribution and concentration of amino acids in hydrothermal sediments.