The proximate composition, fatty acid, and amino acid profile of the body wall and viscera of each red and black sea cucumber (Apostichopus japonicus) from Ulleungdo(Island) and Dokdo(Island) in Korea were compared. Moisture, ash, crude protein, and crude lipid contents ranged between 80.26-91.49, 2.57-6.85, 1.13-3.99, and 0.14-2.12%, respectively. The fatty acid values varied depending on the species and the regions of collection. The anteiso C17:0, C16:$1{Delta}^9$, C17:$1{Delta}^7$, C18:$1{Delta}^{11}$, and C16:$2{Delta}^7$ were only observed in the body wall. Among the tested fatty acids, the C18:$1{Delta}^{11}$ was specific in red sea cucumber, and C20:$4{Delta}^6$ (17.7%) and C20:$5{Delta}^3$ (17.6%) were the predominant polyunsaturated fatty acids (PUFA) in all samples. The contents of the C18:0 dimethyl acetal (C18:0 DMA), C16:$1{Delta}^7$, C16:$1{Delta}^5$, and C18:$1{Delta}^5$ were compared in details. Total amino acids (TAA) of body wall were 1.3-1.9 times higher than those of viscera. Glutamic acid and aspartic acid constituted the major TAA of sea cucumbers. The ratio of essential amino acids (EAA): nonessential amino acids (NEAA) on TAA ranged from 1.15 to 0.67 of sea cucumbers. Viscera of red sea cucumber from Dokdo(Island) were rich in free amino acids (FAA) and showed a high content in leucine.