The evolution of the unique syngnathid male pregnancy has resulted in an array of different brooding types ranging from basic attachment of eggs (pouch-less species: Nerophinae) to specialized internal gestation in pouched species (e.g. Syngnathus and Hippocampus) with many transitions in between. As such it offers a unique platform for assessing adaptations in pregnancy evolution to answer long-standing questions of why and how pregnancy evolved convergently in so many vertebrate systems. To understand the molecular congruencies and disparities in male pregnancy evolution, we compared transcriptome-wide differentially expressed genes in four syngnathid species, at four pregnancy stages (non-pregnant, early, late and parturition).