The dataset contains the counts of megafauna morphotypes annotated on deep sea images from the contract area allocated to the German Federal Institute for Geosciences and Natural Resources (BGR) for the exploration of polymetallic nodules in the Clarion Clipperton Facture Zone, Pacific. A subset of this dataset was used to compute distribution models for 68 megafauna morphotypes (referred to as study 1 in the table). Another subset was used to investigate the influence of habitat heterogeneity on the megafauna composition (referred to as study 2 in the table).