As part of the DAM pilot mission “MGF Ostsee”, the meiobenthic communities of a protected area and a reference area in the Fehmarn Belt (Baltic Sea, Germany) were compared, with both study areas currently permitting mobile bottom trawling (MGF). Meiobenthic data were recorded at the major taxon level, with a special focus on the Copepoda Harpacticoida, which was further examined at the species level. This data collection will serve as a baseline for future assessments, after the planned exclusion of MGF in the protected area in 2024 to identify potential impacts of MGF on meiofaunal communities. In assessing the meiobenthic data in relation to trawling impact, a trawling index derived from multibeam data for the Fehmarn Belt was employed, developed in an early stage of the project. Comparison of major taxonomic levels did not reveal significant differences between the protected and reference areas in terms of taxa composition, abundance values or diversity. However, analysis of the Harpacticoida community at the species level showed that the compared areas differ significantly in species composition and abundance but not in diversity. These differences in the distribution of harpacticoid species indicate a small-scale heterogeneity of different (a)biotic factors. The initial correlation analyses between trawling intensity and both the main taxonomic levels and the Harpacticoida community did not reveal statistically significant results, which is attributable to the relatively small number of samples all recovered in an area affected by trawling. Nevertheless, a higher variance in total abundance between replicates was observed with increasing trawling intensity.