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The complexity of tropical reef habitats affects the occurrence and diversity of the organisms residing in these ecosystems. Quantifying this complexity is important to better understand and monitor reef community assemblages and their roles in providing ecological services. This study employed structure-from-motion photogrammetry to produce accurate 3D reconstructions of eight reefs in Guam and quantified the structural complexity of these sites using seven terrain metrics: rugosity, slope, vector ruggedness measure (VRM), multiscale roughness (magnitude and scale), plan curvature, and profile curvature. The relationships between terrain complexity, benthic community diversity, and coral cover were investigated with generalized linear models. While the average structural complexity metrics did not differ between most sites, there was significant variation within sites. All surveyed transects exhibited high structural complexity, with an average rugosity of 2.28 and an average slope of 43 degrees. Benthic diversity was significantly correlated with the roughness magnitude. Coral cover was significantly correlated with slope, roughness magnitude, and VRM. This study is among the first to employ this methodology in Guam and provides additional insight into the structural complexity of Guam's reefs, which can become an important component of holistic reef assessments in the future. [ABSTRACT FROM AUTHOR]