A highly repetitive interspersed DNA sequence (MRE) was isolated from the genome of medaka, Oryzias latipes, and characterized. Three distinct sequences of MRE were cloned and compared. The conserved sequences of MRE were approximately 220 bp in length. On average, one copy of MRE was present in every 153 kb, and the number of copies of MRE in the genome was calculated to be approximately 9800. MRE constituted approximately 0.14% of the genome. MRE-related sequences were not detected in carp (Cyprinus carpio) red-spot masu trout (Oncorhynchus masou macrostomus), masu salmon (Oncorhynchus masou masou), rainbow trout (Oncorhynchus mykiss), eel (Anguilla japonica), Arctic lamprey (Lampetera japonica), or yellowtail (Seriola quinqueradiata). MRE was randomly distributed in the medaka genome, indicating a high incidence of polymorphism in the five medaka inbred lines.