Aligning the ecological and social dimensions of the connections present between users that harvest a shared natural resource is a necessary step toward sustainable management. However, contrasting estimates of connectivity across disciplines is a challenging task and few empirical studies have focused on population dynamics within fish species with a complex life history. We used a collaborative approach merging citizen science, population genetics, oceanographic modeling, and interviews to collect empirical connectivity data of individual fish, fishing sites, and fishers. We integrated the data within a multilevel social-ecological network framework describing the interactions between two communities of small-scale fishers (Bahia Kino and Puerto Libertad, Sonora, Mexico) targeting leopard grouper (Mycteroperca rosacea). We identified two types of social-ecological links, including the use of specific fishing sites by individual fishers and the harvest of individual fish by individual fishers. Despite their fishing zones not overlapping, the ecological links between two communities located ~150 km apart were consistent and reciprocal where fishing grounds from each community acted as a source of fish to the other during the larval or juvenile/adult stages, respectively. As a result, fishers from the two communities frequently captured fish that were second-degree relatives. In contrast, the probability of social ties among fishers changed significantly depending on the type of connection and was considerably low for leadership and kinship although some communication was present. Our study highlighted how local actions (e.g., recovery from marine reserves or overfishing) are likely to impact the neighboring community as much as locally. The geographic scale and strength of key ecological process supporting fish stocks through the fish life cycle seem to be larger than those of social connections among fishers. Fishers and managers could benefit from a broader regional perspective that strengthens connections between communities about shared goals and activities. We examine some insights learned on the constraints of connectivity given different attributes of each ecological and social component and methodological challenges identified. We also discuss ways to improve collaborative management between the two communities.