The spatial genetic structure of marine organisms is related to dispersal and life-history traits, historical processes, current oceanographic connectivity and habitat features. Here, we assessed the relative importance of these factors for the genetic structure of a broad range of marine species in the Indo Australian Archipelago (IAA). We collated published data on 99 marine species from eight taxonomic groups (ascidians, fishes, molluscs, crustaceans, echinoderms, corals, reptiles, and marine plants) and used generalized linear models (GLMs) to estimate the best predictors of genetic structure. Genetic structure was characterized by FST and the number of genetic clusters over the study area. Predictors tested were: the type of genetic markers; the number of marine ecoregions which are a proxy for habitat variation, historical processes and oceanographic features; species dispersal-related traits (i.e., pelagic larval duration-PLD, adult life habit, reproductive strategy, and egg type); and geographic distance separating populations. The genetic structure of marine species across the IAA was best predicted by traits related to dispersal of larvae or propagules and the mobility of adults; and the number of marine ecoregions sampled not distance was also an important predictor, especially in sedentary and free-swimming species. Our findings highlighted the importance of these key traits to help guide decision-making in spatial management and conservation. There were still many gaps in our understanding of genetic structure, both spatially and within certain taxa, and we recommended future genetic studies focus on habitat-forming taxa and sample sites that are representatively nested in each ecoregion within a marine province or a marine realm, over the spatial extent of the IAA.