Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: , , sp., and sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where and were pre-dominated followed by together with , , and as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. was found as the major bacterial genus across all corals. The lower number of was found in infected with white band disease and sp. with white plaque disease, but marked increases of and , respectively, were observed. This was in contrast to infected by a black band and sp. infected by yellow blotch diseases which showed an increasing abundance of but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.