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Diversity 2011, 4, 581-591; doi:10.3390/d3040581 OPEN ACCESS diversity ISSN 1424-2818 /journal/diversity Article Using DNA Barcoding and Standardized Sampling to Compare Geographic and Habitat Differentiation of Crustaceans: A Hawaiian Islands Example Laetitia Plaisance 1,2, Russell Brainard 3, M. Julian Caley 4 and Nancy Knowlton 1,2,* 1 Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, MRC 163, PO Box 37012, Washington, DC 20013-7012, USA; E-Mail: plaisancel@ 2 Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA 3 NOAA Fisheries, Pacific Islands Fisheries Science Center, Coral Reef Ecosystem Division, 1125-B Ala Moana Blvd., Honolulu, HI 96814, USA; E-Mail: Rusty.Brainard@ 4 Australian Institute of Marine Science, PMB No. 3, Townsville, QLD 4810, Australia; E-Mail: J.Caley@.au * Author to whom correspondence should be addressed; E-Mail: knowlton@; Tel.: +1-202-633-0668; Fax: +1-202-357-3043. Received: 1 July 2011; in revised form: 29 August 2011/ Accepted: 9 September 2011/ Published: 29 September 2011 Abstract: Recently, the Census of Marine Life has explored methods to assess coral reef diversity by combining standardized sampling (to permit comparison across sites) with molecular techniques (to make rapid counts of species possible). To date, this approach has been applied across geographically broad scales (seven sites spanning the Indian, Pacific and Atlantic Oceans