Crustaceans increasingly suffer from the black spot shell disease syndrome, which principally results from bacterial breakdown of their chitinous exoskeleton. Since Cancer pagurus is highly susceptible to this disease, we compared the bacterial communities of black spot affected and non-affected areas of the carapace by amplicon sequencing of 16S rRNA genes and 16S rRNA. Within each spot, bacterial communities of affected areas were less diverse compared to communities from non-affected areas. Communities of different affected spots were, however, more divergent from each other, compared to those of different nonaffected areas. This indicates a reduced and shifted microbial community composition caused by the black spot disease. Different communities found in black spots likely indicate different stages of the disease. In affected areas, Flavobacteriaceae rose up to one of the most abundant and active families, due to massive increase of Aquimarina spp., suggesting a significant role in shell disease syndrome. We isolated 75 bacterial strains from diseased and healthy areas, which primarily affiliated with Proteobacteria and Bacteroidetes, thus reflecting the dominant phyla detected by amplicon sequencing. The ability to degrade chitin was mainly found for Gammaproteobacteria and Aquimarina spp. within the Flavobacteriia, while the ability to use N-acetylglucosamine, the monomer of the polysaccharide chitin, was observed for most isolates, including many Alphaproteobacteria. Furthermore, one third of the isolates showed antagonistic properties. The combination of bacterial community analysis and the physiological properties of the isolates provides insights into a functional complex epibacterial community on the carapace of C. pagurus. Importance In recent years, the shell disease syndrome was detected for several ecologically and economically important crustacean species. Large proportions of populations are affected, e.g., >60% of the widely distributed species Cancer pagurus in different North Sea areas. Bacteria play a significant role in the development of different forms of shell disease, all characterized by microbial chitinolytic degradation of the outer shell. By comparing the bacterial communities of healthy and diseased areas of the shell of C. pagurus we could demonstrate that the disease causes a reduced bacterial diversity within affected areas, a phenomenon co-occurring also with many other diseases. Furthermore, the community composition dramatically changed, with some taxa rising to high relative abundances and showing increased activity, indicating a strong participation in shell disease. Characterization of bacterial isolates obtained from affected and non-affected spots provided deeper insights in their physiological properties and thus the possible role within the microbiome.