Descriptions of microbial diversity in healthy and diseased corals are necessary first steps before further investigating the mechanisms that lead to coral pathology. This is the first study that characterizes the microbial associates from healthy corals to yellow band disease (YBD) lesions using two complementary screening techniques of bacterial 16S rRNA genes [amplified 16S ribosomal DNA restriction analysis (ARDRA) of clone libraries and denaturing gradient gel electrophoresis (DGGE)]. Both these techniques showed similar trends, namely a significant difference in the bacterial community and an increase in diversity from healthy to YBD diseased lesions. There was an increase in the number of sequences retrieved of potentially pathogenic bacteria in diseased tissues compared with healthy samples, most notably from the genus Vibrio. Furthermore, we also detected a number of known pathogenic bacteria within the natural healthy microbiota such as Vibrio carchariae and Vibrio harveyi, a result supporting previous studies, showing healthy corals have the ability to harbour these species.