Background: Viviparity has evolved independently far more than 100 times in vertebrates and over 20 times in fish. Amongst those, several lineages have added to the protection of the embryo inside the body of the mother the provisioning of nutrients and physiological exchange. This required the development of a placenta. One of the most complex organs that serve the function of the embryonal placenta are the trophotaenia of the Goodeid fishes. For a better understanding of this feature and others that make up the remarkable biology of this group of fishes, high quality genomic resources are essential.Results: We have sequenced the genome of a representative species of Goodeids, the Darkedged splitfin, Girardinichthys multiradiatus. The assembly is of chromosome-size and includes the X and Y chromosome. The male-specific region on the Y was identified, allowing some first inferences on the recent origin and the evolution of this peculiar component of the genome. Genome-wide transcriptomic analysis uncovered sex specific differences in brain gene expression and an enrichment for neurosteroidogenesis and testis genes in specifically in male brains. The expression signature of the splitfin embryonal and maternal placenta was established and showed overlap with the human placenta transcriptome, the ovarian follicle epithelium of matrotrophic Poeciliid fish species and the brood pouch epithelium of the seahorse.Conclusion: Our comparative analysis revealed all transcriptomes were enriched for similar pathways and gene categories, in particular those related to transport across membranes, extracellular matrix, cell interactions and metabolism. This result indicates that the development of maternal provisioning as evolutionary novelty repeatedly made use of genes which already in other tissues had the same function. In this way already pre-existing modules are assembled to provide the molecular changes for the novel trait.