Ecklonia cava Kjellman is a common macroalga on rocky reefs in the warm-temperate part of Korea. It often forms dense subsurface canopies, playing an important role as nursery and breeding space for commercial fishes. E. cava surveys were first conducted along a 180 km length of southern Korea between 2003 and 2004, indicated that the external morphology of adult E. cava sporophytes were highly variable along environmental gradients and contributed to confusion about its taxonomy. We quantified the magnitude of morphological and genetic variation in fully developed E. cava across its geographic range in Korea using conservative morphological comparisons and RAPD analysis during the period from March 2007 to May 2007. A total of nine morphological characters were sampled from 6 locations along ~700 km coastline from Jeju Island to Dokdo. All morphological characters investigated were significantly different among locations. There were consistent patterns of spatial variation in individual morphological characters: in most morphological characters, populations (e.g., Yeosu) in turbid nearshore areas and sheltered or semi-exposed showed considerably lower values, compared to those (e.g., Jeju Island) in clear nearshore or offshore areas and semi-exposed or exposed. In addition, most characters were moderately to highly correlated to each other (0.5< R <1.0), suggesting that most morphological characters develop dependently of each other. Multivariate analyses indicated that there were two phenetically distinct groups, and stipe length was the character largely contributing to separating the two groups. For RAPD analysis, a total of 155 discernible and reproducible RAPD bands were generated with 9 selected primers across the 116 individuals of six locations, out of which 56 (36.1%) were polymorphic. The Nei’s diversity (H) varied among locations, ranging from 0.192 to 0.225, with an average value of 0.205. AMOVA showed that the variance components of within and between