Abstract Zooplankton‐microbial interactions play crucial roles in epipelagic ecosystem functions. The distinct west‐to‐east gradients and complex circulation patterns in the Mediterranean Sea, combined with the ubiquity of pelagic copepods, provide an ideal model to study the ecological processes driving host‐associated microbial spatial distribution. Here, we characterized and compared the copepod‐associated microbial metacommunities (CAMC) with those from seawater microbial metacommunities (SMC). Copepod‐associated microbial metacommunities displayed spatial dissimilarity between the western and eastern basins, while SMC exhibited similar microbial compositions. The within‐basin similarity observed in CAMC was associated with connectivity by the surface currents. Ecological drift explained most of CAMC variability, likely as a response to the restricted co‐dispersal of the hosts with their microbes, which presented low prevalence and abundance. Seawater microbial metacommunities displayed higher homogenizing dispersal, with widely distributed generalist taxa. We conclude that CAMC better reflect cross‐basin gradients and connectivity patterns than SMC, suggesting that CAMC may serve as a useful proxy for studying microbial biogeography.