Species lacking distinct secondary sex characteristics, such as differences in size or morphology, are often thought to experience lower levels of sex‐specific selection in comparison to highly sexually dimorphic organisms. 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 have revealed a variety of less easily observed phenotypes that nonetheless 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 distinct secondary sexual characteristics such as size, colour 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. 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 showed higher organ‐specificity in their expression patterns, suggesting that pleiotropic constraints might have historically impacted the evolution of sex‐specific expression patterns. Altogether, we find evidence for ongoing and historical sex‐specific selection in the dusky pipefish.