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The endemic seagrass Halophila hawaiiana Doty & Stone is found in discrete populations throughout the Hawaiian Archipelago. Morphological characteristics of plants from Midway Atoll, Pearl and Hermes Reef, KauaÔi, OÔahu, MolokaÔi, and Maui were measured and compared. Striking variation in leaf length, leaf width, leaf length to width ratio, and internode length was evident among the 18 collection sites sampled at depths ranging from 0.32 to 18 m. DNA sequence analyses of a chloroplast-genome, single-base repeat locus in ramets from nine different collections found only two repeat haplotypes. Repeat haplotypes were fixed at all collection sites and for all islands except O'ahu.