Abstract
The population genetics of the economically important collector urchin, Tripneustes gratilla , were examined in 353 individuals collected from 16 sampling sites throughout Indonesia at 12 microsatellite loci. Bayesian clustering methods over all sampling locations revealed evidence of two genetically distinct clusters, one located predominantly on the shallow Sunda Shelf and the second in the deep waters associated with the biogeographic region known as Wallacea; further analysis revealed additional genetic structure around the island of Halmahera and the Islands of Nias and Mentawai. We propose that the observed genetic differentiation is the result of habitat loss during periods of glacial maxima and differences in physical oceanographic properties throughout the Archipelago. The subsequent recolonization of this habitat as glaciers retreat and sea levels return to present‐day levels creates an unparalleled opportunity for colonists to exploit new habitat. The documentation of cryptic diversity will aid in the identification of hot spots of biodiversity and ultimately its conservation. These data indicate that genetic structure can be detected in a species that has a relatively high dispersal potential, and this differentiation is a potential source of evolutionary novelty.