MicroRNAs (miRNAs, miRs) are short noncoding RNA molecules that negatively control the target mRNAs by binding to the 3' untranslated region (UTR). Previous studies have demonstrated that miR-430 is encoded by a clustered multigene family and is abundantly expressed in early development. In zebrafish, miR-430 is needed to suppress primordial germ cell (PGC)-specific genes, such as nanos1, in somatic cells. However, the molecular characteristics of the miR-430 family in other teleost species have not been reported, and it is unclear whether such a function of miR-430 in PGC specification is a conserved feature of animals or not. In medaka (Oryzias latipes), a distantly related teleost, it has been suggested that PGC might be established in a different mode of specification from that of zebrafish. We characterized 16 miR-430 precursors in the medaka genomic sequence. These miR-430 genes form clusters on chromosome 4, which might share its evolutionary origin with that of the very large miR-430 clusters in zebrafish chromosome 4. However, none of the medaka miR-430 genes are identical to the zebrafish miR-430 paralogs. Medaka miR-430 expression starts during epiboly and decreases after axis formation. Functional analysis using reporter gene constructs showed that miR-430 repressed protein expression by binding to the 3'UTR of zebrafish TDRD7. Consistently, the 3'UTR of medaka TDRD7 contains at least two significant candidates for the putative miR-430 binding site. The ubiquitous and early expression of medaka miR-430 and its ability to downregulate GFP:TDRD7 reporter mRNA imply that miR-430 has a conserved role in early embryogenesis. Smaller copy numbers of miR-430 genes and relatively brief expression in medaka might represent the characteristics of this miRNA family in the common ancestor of teleosts. Changes in the relationships between miR-430 and the target mRNA might be related to differences in the localization patterns of PGC-related genes in medaka and zebrafish.