The functional role of coral-associated bacteria and their contribution to coral health is still largely unknown. The first necessary step to address this gap in the knowledge is based on characterization of the microbial assemblage of the coral and the species-specific, temporal and spatial variation in its diversity. Branched corals (e.g., genus Pocillopora), are the main builders of coral reefs worldwide. This study evaluated the bacteria associated with the mucus and tissues of Pocillopora damicornis and Pocillopora verrucosa, as well as that of the seawater and surrounding sediments, in 6 sites of the Mexican Central Pacific during summer and winter seasons. The molecular techniques DGGE and RFLP were used with the 16S rDNA to assess the most abundant bacterial OTUs. The relationships between the bacterial-coral assemblage and environmental and spatial variables of the reef surroundings were also evaluated, using the multivariate analyses. Twenty different Operational Taxonomic Units (OTU) were obtained, with the highest number presented by the sediments. Specificity of bacterial groups was found for each coral species, as well as between the tissue and mucus of each species. The results showed that the bacterial dominant groups were similar between seasons, but these showed significant spatial variations among substrates within sites, as well as per substrate across all sites. The environmental variables that explained the variation of the dominant bacterial groups in corals and sea water were the coverages of fleshy macroalgae, live coral and sponge. In contrast, variation in the sediments was explained by the coverages of sand, rubble and rock.El papel funcional de las bacterias asociadas a corales y su contribución a la salud del coral es aún desconocido en gran medida. Es necesario que primero se caracterice el ensamblaje microbiano del coral y sus cambios en la diversidad a través de las especies de coral, el espacio y tiempo. Los corales ramificados (e.g., género Pocillopora) son los principales constructores arrecifales a nivel mundial. Este estudio evaluó la estructura bacteriana asociada al mucus y tejidos de Pocillopora damicornis y Pocillopora verrucosa, así como del agua de mar y sedimentos circundantes en 6 sitios del Pacífico central mexicano. Se emplearon las técnicas DGGE y RFLP del ADNr 16S para generar los perfiles de bandeo o evaluar la diversidad. Además, se evaluó la relación del ensamblaje bacteriano-coral con variables ambientales y espaciales del entorno arrecifal (de cada sitio), utilizando análisis multivariados. Se obtuvieron 20 Unidades Taxonómicas Operacionales (OTU) diferentes, siendo los sedimentos los que presentaron mayor número. Se encontró una especificidad de grupos bacterianos para cada especie de coral, así como entre el tejido y mucus de cada especie. Los resultados mostraron que los grupos de bacterias dominantes variaron entre sustratos y entre sitios, encontrando, sólo una variación espacial significativa. Las variables ambientales que explican la variación de los grupos bacterianos dominantes en corales y agua de mar fueron las coberturas de macroalgas carnosas, coral vivo y esponja. En cambio, la variación en los sedimentos fue explicada por las coberturas de arena, escombro y roca