The discovery that the use of PCR with an arbitrarily selected primer to amplify a specific set of arbitrarily distributed loci in any genome laid the foundation for high output of genetic markers that can be used for a variety of purposes. In this study, RAPD was utilized as a method in the identification, interrelationship analysis and the construction of a basic linkage map of medaka (Oryzias latipes). The optimized RAPD-PCR protocol obtained, reveal a moderate degree of genetic diversity among the strains of medaka studied.