Coral disease is one of the major threats to coral assemblages globally and can significantly influence the coral microbiome as a result of climatic and anthropogenic stressors. Coral disease surveys were conducted at three patch reefs in the northern Red Sea of Hurghada coast.  Surveys occurred during a heatwave event in August 2021, when the average surface water temperature reached about 29 °C. This study compared the differences in bacterial communities associated with healthy and diseased coral tissues of nine reef-building coral genera collected from the surveyed reefs. The five most common coral diseases identified were black band disease (BBD), white syndrome (WS), growth anomalies (GA), pink line syndrome (PLS), and skeletal eroding band (SEB).  In general, the microbial abundance in infected parts of corals was higher than that in healthy parts.  Bacteria associated with the black band disease on Platygyra lamellina showed that the number of total bacteria found in the tissue was higher than that in the mucus of the corals. Furthermore, the cultural Vibrio populations (TCBS) of tissue samples were higher than that in mucus samples, and the Vibrio population of the infected coral tissue and mucus was greater than the healthy tissue and mucus. Bacterial 16S rRNA gene clone libraries derived from 12 cultivable isolates of coral mucus and tissue revealed a distinct partitioning of bacterial genera into healthy and diseased samples. Species identified from the healthy samples were dominated by Paracoccus yeei, Staphylococcus aureus, and Acinetobacter sp., while bacteria associated with BBD-affected coral samples were Acinetobacter sp., Desulfovibrio sp., Bacillus farraginis, Vibrio hepatarius, Vibrio brasiliensis, Arcobacter sp., and Micromonospora sp. Our study provides a baseline assessment of coral disease incidence and associated microbial communities in a northern Red Sea region, which is expected to rise as a consequence of increased frequency and severity of climatic and non-climatic stressors.