Rhodolith beds (RBs) are known to increase the seabed complexity and act as a hotspot, supporting a unique biodiversity. This increased structural complexity due to the presence of rhodolith nodules is expected to influence benthic diversity at a local scale. To investigate this further, we tested the hypothesis that high-density rhodolith beds hold higher meiofaunal diversity than low-density beds. We used metabarcoding (V9 hypervariable region from 18S SSU rRNA) on sediment samples from a region with extensive rhodolith beds in the Eastern Brazil Marine Ecoregion, with distinct areas covered by high- and low-density beds. The sediment underneath high-density beds showed higher food availability (biopolymeric carbon) and organic matter quality (protein content and protein-to-carbohydrate ratio); however, meiofaunal composition and phylogenetic diversity was similar among all rhodolith beds sampled in the study area. Shannon's diversity was lower in high-density beds, which may be attributed to the higher organic matter content and quality supporting strong competitors, such as crustaceans and annelids that may dominate and suppress the presence of other meiofaunal taxa. Our results showed that rhodolith beds host a number of meiofaunal zoobenthos that are rarely sampled with traditional morphology-based methods, and we suggest that metabarcoding may become an important complementary method to study rhodolith beds globally. As assessing biodiversity is a prerequisite for any conservation measures, this study can provide insights when managing valuable marine habitats.