Hop (Humulus lupulus L.) is a dioecious climbing plant that is emblematic for the brewing industry because of its specialized metabolites. Many studies have focused on hop metabolism without considering the microbiota associated with hop tissues, although over the past decade, a paradigm shift has redefined plants as holobionts, with complex associations between the plant host and its associated microbial communities. In this study, we investigated the effects of three wild hop genotypes cultivated in two different agricultural soils under controlled conditions on bacterial community composition across different hop compartments (rhizosphere soil, roots, and leaves). Sequencing was performed via Illumina MiSeq with a 2×250 bp paired-end library.