Different marine species and their larvae have characteristics that can expand or contract their potential dispersal, which can add complexity to the management of species assemblages. Here we used a multi-scale biophysical modeling framework, the Connectivity Modeling System, for the analysis of network connectivity for 5 Caribbean coral reef-associated species in order to gauge similarities and dissimilarities among species as well as among Caribbean regions. We estimated local dispersal and retention to assess regional exchanges, and our results revealed that the population structures of coral and fish are different and should thus have dissimilar management requirements in many regions, with some notable exceptions. Populations of Porites astreoides corals appear fragmented, suggesting that loss of adult colonies in any region may significantly impact regional recruitment success and connectivity. At the other end of the spectrum, populations of bluehead wrasse Thalassoma bifasciatum are highly connected, and removal of adults in any single region would not imply future recruitment failure in that region. We suggest using a ‘diversity of exogenous settlement’ index as a proxy of recolonization potential, which is related to the stability of regional connectivity networks. We demonstrate that resolving multispecies larval transport dynamics helps identify regions of both network stability for multi-generational connectivity (e.g. stable larval sources and corridors) pertinent to regional-level management and network inconsistencies among species which are pertinent to the success of local management.