Anthropogenic contaminants with the potential to disrupt biological functions enter aquatic ecosystems from a variety of sources, and pose a potential risk to the long-term sustainability of these ecosystems. Sea urchin embryos and larvae, largely used in developmental biology, have great sensitivity toward environmental perturbations, including several anthropogenic stressors. Much attention has recently been devoted to the sea urchin “chemical defensome,” or genes predicted to be involved in chemical defense to confer resilience and survival to developing embryos, with special attention to the ATP-binding cassette (ABC) transporter genes. The present chapter discusses the role of ABC transporters as the first line of cell defense against both natural and anthropogenic toxicants and their relevance to ecotoxicological studies, including the identification of substrates or inhibitors among natural and anthropogenic toxins and contaminants as well as the circumvention of the multixenobiotic resistance phenotype in realistic exposure scenarios.