Species without dimorphic secondary sex characteristics easily visible to humans, such as difference in size or morphology, are expected to experience low levels of sex-specific selection. However, monomorphism in classic visible traits could be a result of genetic or physiological constraints that prevent the sexes from reaching divergent fitness optima. Additionally, biochemical and molecular work has revealed a variety of less easily observed phenotypes that none-the-less exhibit profound dimorphism. Sex-specific selection could act on these more subtle, less visible, traits. We investigate sex-specific selection in the polygynandrous dusky pipefish (Syngnathus floridae), which lacks size, color, and morphological dimorphism. Using experimental breeding populations, we revealed that although males and females have similar opportunities for sexual selection, only males experience significant sexual selection pressures on body size. We also investigated patterns of sex-biased and sex-specific gene expression in gonads, livers, and gills, and tested whether genes with highly divergent expression patterns between the sexes are more likely to be tissue specific, and therefore relieved of genetic constraints. We. Sex-bias in gene expression was widespread, although the reproductive organs had the most sex-biased and sex-specific genes. Sex-specific selection on gene expression in gills was primarily related to immune response, whereas the liver and gonads had a wide variety of cellular processes, as well as reproductive proteins, showing sex-biased expression. These sex-biased genes are likely less constrained by pleiotropy, as they were more organ-specific in their expression patterns. Altogether, we find evidence for ongoing and historical sex-specific selection in the dusky pipefish.