The dataset contains three files in text (.txt) format or in tabulation-separated value (.tsv) format, that together characterize haplotype composition at the COI locus in the long-spined sea urchin Diadema setosum from the Indo-Malay archipelago. The dataset was produced in the course of a phylogeographic study of this tropical Indo-Pacific species, itself part of IBV’s PhD project on the comparative phylogeography of Indo-Pacific sea-urchins of the genera Diadema and Echinometra. METHODS Briefly, long-spined sea urchins...