Bycatch of marine fauna by small-scale (artisanal) fisheries is an important anthropogenic mortality source to several species of cetaceans, including humpback whales and odontocetes, in Ecuador’s marine waters. Long-term monitoring actions and varied conservation efforts have been conducted by non-governmental organizations along the Ecuadorian coast, pointing toward the need for a concerted mitigation plan and actions to hamper cetaceans’ bycatch. Nevertheless, little has currently been done by the government and regional authorities to address marine mammal interactions with fisheries in eastern Pacific Ocean artisanal fisheries. This study provides a review of Ecuador’s current status concerning cetacean bycatch, and explores the strengths and weaknesses of past and current programs aiming to tackle the challenges of bycatch mitigation. To bolster our appraisal of the policies, a synthesis of fishers’ perceptions of the bycatch problem is presented in concert with recommendations for fostering fishing community-based conservation practices integrated with policies to mitigate cetacean bycatch. Our appraisal, based upon the existing literature, indicates a situation of increasing urgency. Taking into consideration the fishers’ perceptions and attitudes, fisheries governance in Ecuador should draw inspiration from a truly bottom-up, participatory framework based on stakeholder engagement processes; if it is based on a top-down, regulatory approach, it is less likely to succeed. To carry out this process, a community-based conservation programs to provide conditions for empowering fishing communities is recommend. This would serve as an initial governance framework for fishery policy for conserving marine mammals while maximizing the economic benefits from sustainable small-scale fisheries in Ecuador.