What shapes variation in genetic structure within a community of co-distributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in 4 species. Regional structuring (i.e., division of sites into genetically and spatially distinct regions) was most common, detected in 20 species, and nearly all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were non-endemic generalist species. Chaotic structure also associated with relatively high global FST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R2= 0.22), but accounting for higher FST values of chaotic and invertebrate species, compared to regional structuring and fish species, doubled the power of PLD to explain variation in global FST (adjusted R2=0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e., fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawai'i marine species may be generated by demographic variability due to species-specific abundance and migration patterns and/or seascape and historical factors.