Reproductive genes are known to evolve more rapidly than genes expressed in other organs. In this paper we present an overview and bring some new data on the evolutionary study of reproduction-related genes by integrating phylogeny with gene genomic localization. We focus on the gene evolutionary processes of gene birth, death, and divergence. We show that phylogenetic gene birth is confirmed by gene location in genomes, which definitively localized the "place of birth" of new genes (such as Obox and KHDC1/DPPA5/ECAT1/OOEP gene families). By finding their "place of death" in genomes, it also demonstrates that ZP genes TGM4 and OVGP1 have been lost in certain species during vertebrate evolution. Moreover, in the case of gene divergence, comparison of gene locations across different genomes establishes orthologous relationships that are weakly supported by the phylogenetic tree. Specifically, genomic localization demonstrates that the fish and bird mtnr1c (Mel1C) receptor is orthologous to mammalian GPR50, and that ungulate genomes contain new seminal vesicle-specific BSP genes that are not present in other species. Overall, the phylogenomic approach to gene evolution presented in this paper offers more insight into gene function, such as species-specific duplications for speciation, changes in gene expression due to gene divergence, and functional loss by gene death.