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Plant‐associated microbial communities can profoundly affect plant health and success, and research is still uncovering factors driving the assembly of these communities. Here, we examine how geography versus host species affects microbial community structure and differential abundances of individual taxa. We use metabarcoding to characterize the bacteria and eukaryotes associated with five, often co‐occurring species ofSarraceniapitcher plants (Sarraceniaceae) and three natural hybrids along the longitudinal gradient of the U.S. Gulf Coast, as well as samples fromS.purpureain Massachusetts. To tease apart the effects of geography versus host species, we focus first on sites with co‐occurring species and then on species located across different sites. Our analyses show that bacterial and eukaryotic community structures are clearly and consistently influenced by host species identity, with geographic factors also playing a role. Naturally occurring hybrids appear to also host unique communities, which are in some ways intermediate between their parent species. We see significant effects of geography (site and longitude), but these generally explain less of the variation among pitcher communities. Overall, inSarraceniapitchers, host plant phenotype significantly affects the pitcher microbiomes and other associated organisms.