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Corals provide a complex 3D framework that offers habitat to diverse coral reef fauna. However, future reefs are likely to experience reduced coral abundance. Sponges have been proposed as one potential winner on future coral reefs, but little is known of how they contribute to reef 3D structure. Given the ecological importance of structural complexity, it is critical to understand how changes in the abundance of structure-building organisms will affect the three-dimensional properties of coral reefs. To investigate the potentially important functional role of coral reef sponges as providers of structural complexity, we compared the structural complexity of coral- and sponge-dominated areas of an Indonesian coral reef, using 3D photogrammetry at a 4 m2 spatial scale. Structural complexity of 31 4 m2 quadrats was expressed as rugosity indicating reef contour complexity (R), vector dispersion indicating heterogeneity of angles between reef surfaces (1/ k), and fractal dimension indicating geometrical complexity at five different spatial scales between 1 and 120 cm (D 1–5). Quadrats were identified as high- or low-complexity using hierarchical clustering based on the complexity metrics. At high structural complexity, coral- and sponge-dominated quadrats were similar in terms of R and 1/ k. However, smallest-scale refuge spaces (1–5 cm) were more abundant in coral-dominated quadrats, whereas larger scale refuge spaces (30–60 cm) were more abundant in sponge-dominated quadrats. Branching and massive corals contributed the most to structural complexity in coral-dominated quadrats, and barrel sponges in sponge-dominated quadrats. We show that smaller-scale refugia (1–5 cm) are reduced on sponge-dominated reefs at the spatial scale considered here (4 m2), with potential negative implications for smaller reef fauna. • We compared the structural complexity of corals and sponges with 3D photogrammetry. • Tall erect sponges provided overall reef structural complexity comparable to corals. • Refuge spaces 1–5 cm in diameter were supported only by branching corals. • If branching corals decline, sponge dominance may not support small reef fauna. [ABSTRACT FROM AUTHOR]