In the seascape, species migrate between ecosystems to complete their life cycles, such ontogenetic migrations create functional connections between ecosystems. Nevertheless, the scarcity of information on patch distribution, species life history and ecology limit its application in MPA management. We use a potential connectivity model approach to predict how Haemulon flavolineatum might move through a complex and diverse seascape, by simulating part of its life cycle among three ecosystems (reef, mangrove, and seagrass) in the MPA of Bahía Portete-Kaurrele (BPK). We used available ecosystem cover maps to conduct habitat fragmentation analyses and evaluate structural connectivity in BPK (PLAND, LPI, AREA, ENN, NP, SHAPE, CONTAG and IJI indices). With published information on H. flavolineatum home range and its ontogenetic migration distances, we estimated the potential functional connectivity (CONNECT and migration distances) between ecosystems by building bipartite graphs. Patches of different ecosystems were highly intermixed (76%) rather than grouped (58%) reflecting appropriate structural connectivity; particularly for reefs followed by mangrove and seagrass; this seascape promote the potential migration of stage 5, juveniles from mangroves to the reefs (328 links, mainly in the BPK’s southern zone). Meanwhile, the structural configuration could reduce functional connectivity of stage 4 juveniles from seagrass to mangrove (mainly in the northern and central zone; 94 and 49 links respectively). Our model is a novel methodological approach for marine species with ontogenetic migration, which integrates ecological information and the seascape to predict their life cycle. We discuss the need for ecological information of French grunts to validate future models.