An integrated optical and molecular survey was conducted to determine the diversity of bacterial communities inhabiting Montastrea annularis, M. cavernosa, and Diploria strigosa corals infected with black band disease on the leeward reef tract of Curaçao, Netherlands Antilles. PCR amplification and sequencing of microbial 16S rRNA genes with universally conserved rDNA primers identified over 600 bacterial sequences. These isolates represent 12 bacterial divisions that are strongly partitioned amongst the healthy, black band diseased, and dead coral tissues and skeletons, as well as the overlying seawater column. Clone libraries from the black band diseased coral tissue are composed of eight bacterial divisions and 13% unknowns, yet contain only 2% of the same species or strain isolates identified from the healthy and dead coral tissue or the overlying seawater. Sequencing did not detect either Phormidium corallyticum or Beggiatoa spp., which were optically identified as the possible black band disease pathogens in previous studies. Conversely, several bacteria known to be pathogens in other terrestrial and marine organisms were isolated from the black band, including cyanobacteria (Trichodesmium tenue), Cytophagales-Flexibacteria-Bacteroides (Cytophaga fermentans and C. columnaris), and e-proteobacteria (Arcobacter sp.). The presence of Lactobacillus sp., Streptococcus sp., Acrobaster sp., and several terrestrial soil isolates in the black band clone library suggest that human sewage discharge and terrestrial runoff may directly contribute to development of black band disease in scleractinian corals.