The dataset contains counts of meiofauna organisms on high taxonomic level and predicted distributions computed for overall meiofauna abundance, diversity (Simpson's Index D and Evenness E), richness (ntax) and individual taxa using random forest regressions. Furthermore, a habitatmap is provided, dividing the area based on k-means clustering of combined predicted distributions, bathymetry and backscatter. The spatial layers are saved as grid-files, being the standard format of the R-package "raster" (https://cran.r-project.org/web/packages/raster/index.html).Study area is an area allocated to the German Federal Institute for Geosciences and Natural Resources for the exploration of polymetallic nodule mining. Deep-sea mining highly endangers the benthic communities; hence the definition of preservation zones, not only for preservation but also to enable the re-settlement of mined areas, is highly important. These datasets on the spatial distribution of meiofauna have been used to account for a modelling approach to find areas with similar environmental conditions and similar benthic communities.