Twelve morphological characters and the biochemical composition of Undaria pinnatifida f. distans sporophytes growing on the rocky shores of Jindo and Wando and on cultivation ropes in Kijang were measured to determine whether each population could be characterized by morphological features and biochemical composition. The goal of this study was to compare phenotypic variations between populations as they relate to environmental conditions. The sporophytes of the Kijang population were two times longer and 19 times heavier than those at Jindo. Sporophylls of the Jindo U. pinnatifida population were significantly smaller in length, width, frill number, and weight than those at Wando and Kijang. Kijang Undaria plants showed the highest contents of total protein, crude fiber, total amino acids, the amount of essential amino acids, the proportion of total unsaturated fatty acids, and eicosapentaenoic acid. However, the Jindo population showed the greatest content of carbohydrates, lipids, and minerals (Zn and Ca) of the three U. pinnatifida populations. In particular, Zn content of Jindo plants was 30 times greater than that of Kijang plants. Thus, the proximate composition, mineral composition, amino acids, and fatty acids of Undaria pinnatifida plants were distinguishable among the three representative Undaria populations evaluated. These results suggest that morphological and biochemical differences of the three U. pinnatifida populations can be attributed to differences in environmental conditions of their habitats.