The gene nanos is essential for germ cell development. Although its functions and expression have been investigated in the mouse, nanos genes have yet to be well characterized in other vertebrates. Based on similarity and a syntenic analysis of nanos, we have identified four different nanos in the genome of medaka (Oryzias latipes). nanos1 is duplicated in teleost fish genomes and named nanos1a and nanos1b. Of all medaka nanos, nanos3 is well conserved in terms of expression and synteny. In contrast to a previous study on mice, nanos2 expression was not detected in the gonads at early stages of sex differentiation; however, both oogonia and spermatogonia in adult gonads exhibit nanos2 expression. nanos1a and 1b are both expressed in the developing brain, consistent with the expression of nanos1 in mice. In the gonads, nanos1a is expressed in the somatic cells surrounding oocytes and spermatocytes, whereas expression of nanos1b is not detectable in the gonads by in-situ hybridization. These results suggest common and distinct functions of nanos genes among vertebrates.