Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of theEndozoicomonadaceaefamily. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology ofEndozoicomonadaceaeat an ocean basin-scale by sampling specimens from three coral genera (Pocillopora,Porites,Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species ofEndozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found inPocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage inPocilloporaand mainly by the geographic location inPorites.Milleporais more rarely associated toEndozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceaeassociations that are defined at the bacteria lineage level.