Interactions between hermatypic corals and bacterial communities on the coral surface play key roles in shaping coral health and disease. Recent studies have suggested that dynamics of the surface bacterial community in terms of species composition and metabolism exert considerable impacts on the disease development on the coral. In order to better understand the dynamics of surface bacteria, we aimed to monitor the bacterial community structure on the surface of Acropora muricata by DGGE and clone library analyses. In 2010, we monthly collected branches of A. muricata from Okinawa Churaumi Aquarium, Japan and PCR-amplified 16S rRNA genes from DNA extracted from the coral specimens. DGGE resulted in the detection of bacterial genera, such as Acinetobacter and Sphingomonas. Clone library analysis also supported persistent presence of Acinetobacter in each month, and revealed occasional presence of other genera, including Endozoicimonas, Spongiobacter and Vibrio. These results demonstrated that bacterial community on A. muricata surface was comprised of diverse types of bacteria that may be benign or pathogenic to the coral. Further identification of the bacterial components is clearly needed to gain deeper insights into interactions not only among the bacteria, but also between the bacteria and the coral.