Consistent hatchery production of marine fish continues to be one of the critical bottlenecks in the growth of this sector of the aquaculture industry. This is particularly true for production of high-value, yet challenging to rear, pelagic fish species such as mahi-mahi (Coryphaena hippurus) and tuna (Thunnus). In many cases, the difference between success or failure in development of hatchery technology for marine fish species comes down to how well understood the species is at all early life stages from ontogenetic and physiological standpoints. Inadequate understanding of the species-specific differences in organogenesis, growth patterns, nutritional demands, and behavior, among other factors, serve to limit the production potential of challenging species. Put simply, some marine fish species are more forgiving than others. There are many species that have historically been identified as having high market potential, yet reliable commercial-scale hatchery production has yet to be realized. However, advances in ontogenetic and physiological research have allowed for new insights into many of these challenging fish species, thereby allowing producers to make substantial improvements in developing hatchery technology for them. Findings from utilization of these advancements in a variety of marine fish species, such as mahi-mahi, will be presented. Information that is key to improving marine fish hatchery production, such as examination of the activity levels of selected digestive enzymes during ontogeny, will also be discussed for different species. Additionally, results will be presented detailing how such information can be utilized effectively to optimize marine fish hatchery production, particularly in the case of high-value candidate species. Many of the findings from early life stage ontogenetic and physiological research have provided valuable insights that extend beyond benefits in hatchery production, leading to further improvements in nursery and grow-out stages. Species-specific examples will be presented and discussed.