Two reef systems off south Molokai, Hale O Lono and Hikauhi (separated by only 10 km), show strong and fundamental differences in modern ecosystem structure and Holocene accretion history that reflect the influence of wave-induced near-bed shear stresses on reef development in Hawaii. Both sites are exposed to similar impacts from south, Kona, and trade-wind swell. However, the Hale O Lono site is exposed to north swell and the Hikuahi site is not. As a result, the reef at Hale O Lono records no late Holocene net accretion while the reef at Hikauhi records consistent and robust accretion over late Holocene time. Analysis and dating of 24 cores from Hale O Lono and Hikauhi reveal the presence of five major lithofacies that reflect paleo-environmental conditions. In order of decreasing depositional energy they are: (1) coral-algal bindstone; (2) mixed skeletal rudstone; (3) massive coral framestone; (4) unconsolidated floatstone; and (5) branching coral framestone-bafflestone. At Hale O Lono, 10 cores document a backstepping reef ranging from ϳ 8,100 cal yr BP (offshore) to ϳ 4,800 cal yr BP (nearshore). A depauperate community of modern coral diminishes shoreward and seaward of ϳ 15 m depth due to wave energy, disrupted recruitment activities, and physical abrasion. Evidence suggests a change from conditions conducive to accretion during the early Holocene to conditions detrimental to accretion in the late Holocene. Reef structure at Hikauhi, reconstructed from 14 cores, reveals a thick, rapidly accreting and young reef (maximum age ϳ 900 cal yr BP). Living coral cover on this reef increases seaward with distance from the reef crest but terminates at a depth of ϳ 20 m where the reef ends in a large sand field. The primary limitation on vertical reef growth is accommodation space under wave base, not recruitment activities or energy conditions. Interpretations of cored lithofacies suggest that modern reef growth on the southwest corner of Molokai, and by extension across Hawaii in general, is controlled by wave-induced near-bed shear stress related to refracted North Pacific swell. Holocene accretion patterns here also reflect the long-term influence of wave-induced near-bed shear stress from north swell during late Holocene time. This finding is consistent with other studies (e.g., Grigg 1998; Cabioch et al. 1999) that reflect the dominance of swell energy and sea level in controlling modern and late Holocene accretion elsewhere in Hawaii and across the Pacific and Indian oceans. Notably, however, this result is refined and clarified for Hawaii in the hypothesis of Rooney et al. (2003) stating that enhancement of the El Niño Southern Oscillation beginning approximately 5000 years ago led to increased north swell energy and signaled the end to net accretion along exposed coastlines in Hawaii. The exposure of Hale O Lono to north swell and the age of sea floor there (ca. 4,800 cal yr BP), coupled with the lack of north swell incidence at Hikauhi and the continuous accretion that has occurred there over the last mill...