In this project (2011–2015), we studied larval transport and population connectivity of a fish (damselfish, Dascyllus aruanus) and an invertebrate (giant clam, Tridacna maxima) species in the South Lagoon of New Caledonia (SLNC) using three emerging and complementary approaches: (1) parentage analysis via genetic fingerprinting, (2) microchemical analysis of trace elements and artificial markers, and (3) biophysical, metapopulation and genetic models of larval transport and its consequences for population dynamics. While these three fields have independently made many significant advances recently, few, if any, studies have integrated these approaches into a single analysis of marine connectivity patterns. In particular, while understanding connectivity is essential for answering many management and scientific questions, such as achieving effective spatial management of marine resources (e.g., marine protected areas -MPAs-) and understanding the spatial structuring of marine ecosystems, there is a significant gap between our ability to experimentally measure connectivity (e.g., through ecological, genetic and microchemical studies) and our ability to model larval transport (e.g., through biophysical models). To contribute bridging this formidable gap, we brought together a group of young researchers with diverse and complementary skills to attack this problem from a variety of angles. The SLNC provides an ideal model system for studying connectivity on a manageable spatial scale, as well as poses a number of pressing management problems, such as assessing MPA effectiveness and conserving threatened marine species and ecosystems.