Two cDNA clones encoding alpha and beta subunits of soluble guanylyl cyclase (GC) were isolated from medaka fish (Oryzias latipes) cDNA libraries and designated as OlGCS-alpha1 and OlGCS-beta1, respectively. The ORF of OlGCS-alpha1 encodes 678 amino acids and that of OlGCS-beta1 encodes 614 amino acids. Both subunits have a putative catalytic domain conserved with membrane GC and adenylyl cyclases. The amino acid sequences of OlGCS-beta1 and mammalian soluble GC subunits are highly conserved throughout the entire protein, suggesting that amino acid sequences outside the catalytic domain are important for the functioning of the beta subunit. On the contrary, amino acid sequences of alpha subunits outside the catalytic domain are fairly divergent between fish and mammals. Reverse transcription/PCR (RT/PCR) analysis showed that OlGCS-alpha1 and OlGCS-beta1 transcripts were abundant in the brain, eye, spleen and testis. RT/PCR analysis demonstrated that both transcripts were present in unfertilized eggs, were reduced immediately after fertilization, then increased again. In addition, our results suggest that expression patterns of OlGCS-alpha1 and OlGCS-beta1 genes are different from each other both during development and in adults.