Molecular breeding, leveraging DNA testing, plays a pivotal role in facilitating the crossing, selection, and quality assurance processes within selective breeding and production programs. Demonstrated to augment genetic gains while conserving time, resources, and finances, this approach enhances product quality, success rates, and time-to-market across diverse sectors of natural-based commodities. The integration of molecular breeding into aquaculture, similarly to other industries, presents unique challenges. In this presentation, we will delineate these challenges and propose viable solutions, drawing insights from recent endeavors focused on Crassostrea virginica oysters.