Abstract Successful long‐term conservation relies on strategic planning for pragmatic actions to mitigate threats. Prioritizing actions and areas to support conservation goals in the most cost‐effective scenario becomes crucial in resource‐limited environments. However, planning and management can be challenging in data‐limited contexts. Incorporating local ecological knowledge (LEK) into conservation planning is an underexplored method of addressing these knowledge gaps. We utilized systematic conservation planning to identify key sites for seahorse threat management in a complex social‐ecological system in a protected area. Through participatory mapping and interviews with artisanal fishers, we gathered insights about seahorses, threats to them, and their socioeconomic significance for the local community. We compared LEK‐derived seahorse conservation priorities with spatial priorities identified using Marxan and with LEK‐derived and science‐derived data to explore LEK's contribution to spatial planning for a data‐poor species and to explore different seahorse threat management scenarios. The LEK‐derived and science‐derived seahorse abundance Marxan scenarios had a strong spatial agreement, emphasizing LEK's role in conservation planning. Furthermore, LEK‐derived data filled key data gaps on the distribution and nature of water‐based threats. Threat management scenarios for land and water‐based threat management had distinct spatial patterns. Incorporating LEK into decision‐making empowered local communities and thus fostered community‐based management. These findings offer insights into conservation planning in data‐deficient scenarios and can aid decision makers and local stakeholders in inclusive conservation strategies. Our results identified priorities for seahorse conservation in the Rio Formoso Estuary and our methods offer a transferable approach for participatory and interdisciplinary planning, which are essential for biodiversity conservation and livelihoods maintenance.