Recently, a compost fermented with marine animals with thermophilic Bacillaceae in a clean and exclusive process at high temperature was reported as a possible feed additive to improve the healthy balance in sea fish and mammals (i.e., pigs and rodents). Here, the effects of the oral administration of the compost on the muscle and internal organs of carp (Cyprinus carpio) as a freshwater fish model were investigated. The fatty acid composition was different in the muscle of the carp fed with or without the compost extract, but there was little difference in the hepatopancreas. The accumulation of triacylglycerols, cholesterol, lipid peroxide and hydroxyl lipids decreased in the muscle after the oral administration of the compost extract in the carps over 12 weeks, but the accumulation did not always decrease in the hepatopancreas. In contrast, free-radical-scavenging activities and the concentrations of free amino acids in the muscle did not always increase and was dependent on the dose of the compost at 12 weeks. The scavenging activities and part of free amino acid levels in the muscle of the carp were improved at 24 weeks after a high dose of compost exposure, and then the survival rates of the carp were maintained. Thus, the oral administration of thermophile-fermented compost can prevent peroxidation and increase the content of free amino acids in the muscle of the freshwater fish, depending on the dose and term of the administration, and may be associated with the viability of the fish. (C) 2015, The Society for Biotechnology, Japan. All rights reserved.