Understanding how meiofaunal communities respond to spatial protection measures is essential for evaluating the effectiveness of marine conservation strategies, particularly in heavily impacted regions such as the Baltic Sea. Here, we present one of the first integrated assessments of meiofaunal diversity across marine protected areas (MPAs) and adjacent reference areas (REFs) in the Baltic Sea. Our study combines whole-community metabarcoding of two genetic markers—mitochondrial COI and ribosomal 18S—with classical morphological identification of harpacticoid copepods. Sampling was conducted in the Fehmarn Belt and Oderbank regions as part of the DAM pilot mission MGF Ostsee, prior to the exclusion of mobile bottom-contact fishing. We provide a valuable baseline of community composition under current conditions. Results highlight strong complementarity between the genetic markers: 18S offered broader taxonomic coverage and higher alpha diversity, particularly for Nematoda and Platyhelminthes, while COI enabled more precise species-level resolution, especially for Copepoda. Spatial analyses revealed distinct assemblages between Fehmarn Belt and Oderbank, with notably higher copepod diversity in Fehmarn Belt. Significant differences between MPAs and REFs were detected only in Oderbank. Morphological and molecular datasets showed substantial but incomplete overlap, with each method capturing unique taxa, demonstrating their combined value for comprehensive biodiversity assessments. Our findings suggest that meiofauna communities reflect both regional environmental gradients and high small-scale patchiness. This study underscores the utility of multi-marker metabarcoding alongside traditional taxonomy for monitoring meiobenthic diversity and highlights the importance of incorporating meiofauna into long-term ecological assessments. The dataset provides a crucial reference point for evaluating future recovery and management outcomes following trawling exclusion.
