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Abyssal polymetallic nodule fields represent a unique deep-sea habitat. The hard substratum provided by nodules is thought to increase habitat complexity, promoting the occurrence of highly diverse abyssal assemblages. However, hard substratum in these habitats is also available as outcropping rock fragments, but their contribution to habitat heterogeneity has been largely overlooked. Here, we assessed if the type and size of hard substratum can modulate benthic biodiversity at local scales within the Clarion Clipperton Zone (N Pacific abyss). We compared megafauna (animals >10 mm) assemblages in nodule bearing habitats with those in areas containing rocks in addition to nodules. We found a lower faunal density but a clearly higher diversity and more heterogenous composition in the assemblages of rock bearing areas compared to those with only nodules. In addition, hard substratum patch size appeared to positively influence the size of some taxa, like bamboo corals. These results suggest that rocks, in addition to nodules, constitute keystone structures enhancing habitat heterogeneity at local scales within nodule fields. Rock areas appear common in some abyssal plains and may make regionally-important contributions to abyssal biodiversity, suggesting that they may be relevant to include in conservation efforts.