Planktonic larvae were captured above a shallow coral reef study site on the Great Barrier Reef (GBR) around spring-summer new moon periods (October-February) using light trap or net capture devices. Larvae were identified to the genus or species level by comparison with a phylogenetic tree of tropical marine fish species using mtDNA HVR1 sequence data. Further analysis showed that within- species HVR1 sequence variation was typically 1-3%, whereas between-species variation for the same genus ranged up to 50%, supporting the suitability of HVR1 for species identification. Given the cur- rent worldwide interest in DNA barcoding and species identification using an alternative mtDNA gene marker (cox1), we also explored the efficacy of different primer sets for amplification of cox1 in reef fish, and its suitability for species identification. Of those tested, the Fish-F1 and -R1 primer set recently reported by Ward et al. (2005) gave the best results.