The economic resources available for conservation are limited, so conservation projects must have solid planning elements to ensure their effectiveness. In this regard, the design and planning of the 14 priority species recovery plans in Mexico were evaluated. In addition, the implementation of the manatee conservation program was evaluated as a case study. It was observed that the plans have deficiencies in their formulation of objectives, goals, and prioritization of threats. In all the recovery plans, the management strategies are not linked to objectives and goals, or the mitigation of threats. The importance of the technical committee was assessed, since it implemented 38% of the actions featured in the recovery plan. This is despite the lack of funding from the federal government. It was determined that the main obstacle to the effectiveness of the plans was the lack of institutional capacities of the federal environmental agencies, specifically regarding the following: (1) Insufficient economic resources, (2) Inadequate human resources, and (3) Limited capacities in planning, monitoring, and project evaluation.