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Background  The marine medaka  Oryzias melastigma  has been demonstrated as a novel model for marine ecotoxicological studies. However, the lack of genome and transcriptome reference has largely restricted the use of  O. melastigma  in the assessment of  in vivo  molecular responses to environmental stresses and the analysis of biological toxicity in the marine environment. Although  O. melastigma  is believed to be phylogenetically closely related to  Oryzias latipes , the divergence between these two species is still largely unknown. Using Illumina high-throughput RNA sequencing followed by  de novo  assembly and comprehensive gene annotation, we provided transcriptomic resources for the brain, liver, ovary and testis of  O. melastigma . We also investigated the possible extent of divergence between  O. melastigma  and  O. latipes  at the transcriptome level.    Results  More than 14,000 transcripts across brain, liver, ovary and testis in marine medaka were annotated, of which 5880 transcripts were orthologous between  O. melastigma and O. latipes . Tissue-enriched genes were identified in  O. melastigma , and Gene Ontology analysis demonstrated the functional specificity of the annotated genes in respective tissue. Lastly, the identification of marine medaka-enriched transcripts suggested the necessity of generating transcriptome dataset of  O. melastigma .    Conclusions  Orthologous transcripts between  O. melastigma  and  O. latipes , tissue-enriched genes and  O. melastigma -enriched transcripts were identified. Genome-wide expression studies of marine medaka require an assembled transcriptome, and this sequencing effort has generated a valuable resource of coding DNA for a non-model species. This transcriptome resource will aid future studies assessing  in vivo  molecular responses to environmental stresses and those analyzing biological toxicity in the marine environment.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1325-7) contains supplementary material, which is available to authorized users.

Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes