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. Meiofauna samples were collected with a multicorer (MUC) on the expedition EMB238 of RV ELISABETH MANN BORGESE from May 26th to June 9th, 2020. From each MUC core the upper 5 cm of the sediment and the supernatant water filtered over 40 µm were used for further processing (area coverage per core: 72.4 cm²). For the morphological approach, this material was fixed with buffered formalin (final concentration: about 4%). Subsequently, in the laboratories of the German Centre for Marine Biodiversity Research (DZMB) in Wilhelmshaven, further treatment took place, namely centrifugation of the rinsed samples with Levasil®, a colloidal gel, to separate the organisms from the sediment (cf. McIntyre and Warwick 1984). Because the sampling material contained an extraordinary abundance of meiofauna, each sample had to be divided into sub-samples before counting and sorting the organisms to ensure efficient processing. This was done using the Jensen splitter (Jensen 1982), which divides a sample into eight equally sized sub-samples. One of these was randomly selected and used for further evaluation. For the identification and counting of the individuals, we used Leica DMR and Leica DM 2500 microscopes with interference contrast.