Marine environments are highly heterogeneous, varying across scales of a few meters to entire ocean basins. Understanding the relationship between environmental variability and species distribution is essential for area‐based management and conservation. However, this requires a precise alignment of seabed mapping with environmental and biological sampling, which is often difficult to achieve in the deep sea. There is thus an urgent need to tackle this challenge to effectively manage high‐diversity habitats such as deep‐sea coral and sponge aggregations. Relying on multiple subsea platforms, seafloor mapping, and imaging techniques, we mapped the distribution of megafaunal communities at Sur Ridge (780–1525‐m depth; off central California) across multiple spatial scales. First, remotely operated vehicle video transects were conducted to characterize community distribution along the ridge in relation to substratum type, environmental conditions, and 1‐m resolution bathymetry. Five distinct communities, located in specific areas of the ridge, were identified. These communities were primarily structured by depth, availability of hard substrata, and terrain complexity (slope and rugosity). Indicator taxa were identified for each community and their distributions were characterized at the centimeter scale from coregistered 5‐mm resolution photomosaic and 5‐cm lateral resolution bathymetry produced during low altitude remotely operated vehicle surveys. High‐resolution mapping allowed the identification of associations between deep‐sea coral and sponge and other benthic taxa and showed that, even at these small scales, different taxa associate with distinct microhabitats. These results highlight the importance of accounting for habitat heterogeneity, and its role in supporting biodiversity when designing management and conservation strategies.