The recent isthmus close causing the Tropical Eastern Pacific Ocean (TEP) becomes a nutrient rich ecosystem, where the Pacifigorgia sympatric octocorals take advantages to environmental adaptation. Panama isthmus offers a natural evolutionary experiment to identify processes implied in octocoral-microbiome evolution. Mechanisms through bacterial communities affect the host evolutionary trajectory and how evolved the symbiosis octocoral-microorganism are poor study. We studied bacterial communities of 13 sympatric Colombian species of Pacifigorgia to search eco-evolutionary patterns. We demonstrate that microbiome is an important evolutionary trait of the host, found phylosymbiotic and cophylogeny patterns, where some species of Pacifigorgia are dominated by a single bacterial phylotypes with significant phylogenetic signal across Pacifigorgia history. Some bacteria are specie-specific, where bacterial functional profiles differ between Pacifigorgia species. The bacterial community is a driving force affecting evolutionary host history, consolidating a potential coevolution scenario where Pacifigorgia octocorals are presumably undergoing an adaptive radiation in response to ecological opportunities in which microbiomes are shaped by the host and recapitulated host evolutionary processes