This dissertation work presents a novel method for addressing system uncertainty to improve management of a small-scale fishery in St. Croix, United States Virgin Islands. Using fishers' ecological knowledge (FEK), this research examines existing perspectives and biases through the Q-Method to identify regulatory inefficiencies in the management framework and strengthen the rationale for including fishers into the management process, develops a coupled behavior-economics model to predict the likelihood of fishing the preferred grounds under a range of physical and regulatory conditions, establishes a baseline assessment of a spawning aggregation of mutton snapper following sixteen years of protection through a no-take marine protected area, and conducts a discrete choice method test to examine likely public support for FEK-based proposed regulatory alternatives. This work contributes to an under-studied and much-needed area of fisheries management, that of incorporating socioeconomic motivations within an ecosystem-based framework. As fisheries management efforts begin to embrace ecosystem-based approaches, the need for understanding and incorporating the knowledge and behavior of fishers into management has never been greater. Ecological goals of fishery sustainability and continued habitat function cannot be achieved without first understanding how fishers view and respond to any regulatory environment and then developing a framework that achieves the greatest support for those regulations. The time has come for incorporating FEK into ecosystem-based fisheries management.