The perpetuation and preservation of distinct species rely on mechanisms that ensure that only interactions between gametes of the same species can give rise to viable and fertile offspring. Species-specificity can act at various stages, ranging from physical/behavioral pre-copulatory mechanisms, to pre-zygotic incompatibility during fertilization, to post-zygotic hybrid incompatibility. Herein, we focus on our current knowledge of the molecular mechanisms responsible for species-specificity during fertilization. While still poorly understood, decades of research have led to the discovery of molecules implicated in species-specific gamete interactions, starting from initial sperm-egg attraction to the binding of sperm and egg. While many of these molecules have been described as species-specific in their mode of action, relatively few have been demonstrated as such with definitive evidence. Thus, we also raise remaining questions that need to be addressed in order to characterize gamete interaction molecules as species-specific.