This study compares percentage cover of benthic organisms at the species level at Pearl and Hermes Atoll (PHA), the largest atoll in the Northwestern Hawaiian Islands, to determine (1) the degree of difference among sites, (2) whether wave-exposure zones explain observed patterns in benthic community structure, and (3) whether species richness differs among wave-exposure zones. Thirty-four sites were surveyed representing four categorical waveexposure regimes: high, intermediate-high, intermediate-low, and low. A twoway nested analysis of similarity (ANOSIM) found significant differences among sites and that wave exposure explained some, but not all, of this variation. High and low wave-exposure zones were found to differ significantly from other zones. Low wave-exposure sites exhibited the highest similarity to each other and were dominated by the finger coral Porites compressa (38% cover). High wave-exposure sites were also similar to each other and were dominated by crustose coralline red algae (37% cover). Sites within the intermediate-high zone exhibited substantial variability; however, the presence of the green alga Microdictyon setchellianum was a unifying characteristic among many sites in this zone. Finally, intermediate-low wave-exposure sites exhibited the greatest degree of variability among sites and also exhibited the greatest level of benthic species diversity, including presence of rarer species. Wave exposure proved a useful tool in describing the diverse assemblages of benthic communities at PHA, especially for sites experiencing extreme high and low wave exposure.