|Abstract||Syngnathid fishes (sea horses, pipefish, and sea dragons) are a group of organisms that exhibit several unusual behaviors such as male brooding and sex-role reversal. Most sex-bias gene expression studies have been done on species that exhibit traditional sex-roles (male-male competition) where females invest more parental time than males. Here we use the Gulf pipefish (Syngnathus scovelli) which exhibits female-female competition for mates along with male brooding to look at sex-biased expression. We used RNA-seq technology to build the first transcriptome of the brain and gills of this species using four mature male and three mature female pipefish from Port Lavaca Bay, Texas. Differential gene expression analysis returned 73 differentially expressed genes (DEGs) in the brain and 29 DEGs in the gill. In the brain, there were 26 DEGs upregulated in females and 47 upregulated in males. In the gills, there were 10 DEGs upregulated in females and 19 upregulated in males. Gene Ontology analysis found many pathways altered between the brain and gill transcriptomes. We focused on three areas of interest in the sex-bias gene expression field which included sex steroids/hormones in the brain, circadian rhythms, and immunity. We found a few genes differentially expressed for all these categories. In addition, this novel transcriptome will help in conservation efforts of threatened species from this family via its use in identifying polymorphic markers. Such markers may prove valuable in surveying population structure and genetic variability.--Abstract.