© 2020, Senckenberg Gesellschaft für Naturforschung. We analysed the genetic connectivity and larval transport routes of Lutjanus argentiventris to test if eddies could transport coastal-demersal fish larvae between the peninsular and mainland coasts of the Southern Gulf of California. Larval transport was estimated using the ROMS oceanographic model during the main spawning period (July–August). We used 12 microsatellite loci to assess genetic diversity, population structure and gene flow estimates in 233 L. argentiventris samples from nine sites. The oceanographic model suggested the existence of a stream flow and eddies that maintain connectivity in the Southern Gulf of California. The global AMOVA and paired FST showed no significant genetic differentiation among the sites, and the estimations of the number of migrants indicated moderate to high gene flow among locations. However, after testing five demographic scenarios of connectivity with a coalescent sampler, our results supported the presence of a metapopulation structure with source-sink dynamics. We discuss the challenges to reconcile our results considering the assumptions of the different analyses and the characteristics of marine metapopulations. Connectivity of L. argentiventris could be representative of other costal-demersal species with a similar life history and spawning season.