Seahorses and pipefish are characterized by different forms of male pregnancy, a complex morphological and physiological process akin a mammalian pregnancy. The genetic regulation of this complex trait, however, is unknown, complicating our efforts to understand how this trait has evolved. To permit such studies, the processes of male pregnancy have been reviewed, and the genes of male pregnancy have been identified using cDNA-AFLP based differential displays and next generation sequencing technology. Initial efforts to identify gene expression differences during male pregnancy using a novel cDNA-AFLP endlabelling protocol proved unsuccessful, and an extensive eukaryote-wide computer-based optimization study was undertaken to optimize the cDNA-AFLP methodology for species in which genome data are unavailable. Next generation sequencing was ultimately used to identify the genes of male pregnancy. More than 38,000 cDNA fragments have been sequenced and annotated wherever possible. Hundreds of genes up- and downregulated during male pregnancy were identified, and major gene functions have been associated with these genes. As a result, a more circumspect picture of both processes and the genes involved in male pregnancy in the seahorse is available. This thesis is structured into four chapters. Chapters I and III have been published in peer reviewed international journals. Chapters II and IV are being prepared for submission.