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Background  The annual fish  Nothobranchius furzeri  is characterized by a natural dichromatism with yellow-tailed and red-tailed male individuals. These differences are due to different distributions of xanthophores and erythrophores in the two morphs. Previous crossing studies have showed that dichromatism in  N. furzeri  is inherited as a simple Mendelian trait with the yellow morph dominant over the red morph. The causative genetic variation was mapped by linkage analysis in a chromosome region containing the  Mc1r  locus. However, subsequent mapping showed that  Mc1r  is most likely not responsible for the color difference in  N. furzeri . To gain further insight into the molecular basis of this phenotype, we performed RNA-seq on F2 progeny of a cross between  N. furzeri  male and  N. kadleci  female.    Results  We identified 210 differentially-expressed genes between yellow and red fin samples. Functional annotation analysis revealed that genes with higher transcript levels in the yellow morph are enriched for the melanin synthesis pathway indicating that xanthophores are more similar to melanophores than are the erythrophores. Genes with higher expression levels in red-tails included xanthine dehydrogenase ( Xdh ), coding for a biosynthetic enzyme in the pteridine synthesis pathway, and genes related to muscle contraction. Comparison of DEGs obtained in this study with genes associated with pigmentation in the Midas cichlid ( A. citrinellus ) reveal similarities like involvement of the melanin biosynthesis pathway, the genes  Ptgir ,  Rasef  (RAS and EF-hand domain containing), as well as genes primarily expressed in muscle such as  Ttn  and  Ttnb  (titin, titin b).    Conclusions  Regulation of genes in the melanin synthetic pathway is an expected finding and shows that  N. furzeri  is a genetically-tractable species for studying the genetic basis of natural phenotypic variations. The current list of differentially-expressed genes can be compared with the results of fine-mapping, to reveal the genetic architecture of this natural phenotype. However, an evolutionarily-conserved role of muscle-related genes in tail fin pigmentation is novel finding and interesting perspective for the future.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-754) contains supplementary material, which is available to authorized users.

Transcriptome profiling of natural dichromatism in the annual fishes Nothobranchius furzeri and Nothobranchius kadleci