Reef-building corals are susceptible to black band disease (BBD), an infection characterized by a cyanobacteria-dominated microbial mat that kills coral tissue. BBD mats infecting six scleractinian corals and one gorgonian were studied to assess and identify important microbes involved in the disease. Genotypic variability of dominant BBD cyanobacteria was analyzed at high resolution using cyanobacteria-specific terminal restriction fragment length polymorphism (TRFLP) analysis of the rRNA internal transcribed spacer (rRNA-ITS) region. Most coral species were dominated by one of two distinct genotypes of the common BBD cyanobacteria CD1C11. The BBD mat infecting the seafan Gorgonia ventalina Linnaeus, 1758 was dominated by different cyanobacteria genotypes (SFDC1 and SFDC2). Clone library sequencing and TRFLP analyses of rRNA genes and reverse-transcribed rRNA reveal the identity and activity of the most abundant BBD microbes. A potential role of these microbes in infection and immunity was studied by comparing the microbial communities of BBD mats to those associated with the healthy tissues of infected and non-infected corals. The dominant cyanobacteria genotype CD1C11 was detected on healthy tissues of several diseased coral species, as well as on healthy colonies showing no outward signs of disease. Other important constituents of the BBD mats included Rhodobacteraceae, Vibrionaceae, and Bacteroidetes. Several isolates were similar to genotypes associated with other coral diseases.