Rhizosphere microbiome critically influences plant growth and health, yet the genetic mechanisms underlying host regulation of microbiome composition remain unclear. Here, we analyzed whole-genome genotype and 16S rhizosphere microbiome data from 432 globally sourced eggplant accessions (Solanum melongena L.). Eggplant population structure corresponded to geographic origins, with rhizosphere microbiomes varying significantly among subpopulations. Host genetics explains 9%–39% of the variation in individual microbial taxa abundance, with core taxa more affected by host genetic variation. Microbial genome-wide association studies (mGWAS) identified 1235 significant genetic variants associated with 46 core microbial taxa, revealing key regulatory loci including chr10:7799021 near MYB113 (associated with Stenotrophomonas, P = 2.16 × 10−15) and chr10:19786889 near BLH9 (associated with Mycobacterium, P = 1.24 × 10−12), as well as a chromosome 5 locus with specific regulatory effects on Rhizobiales. These microbiome-associated genetic variants were enriched in secondary metabolic pathways, including anthocyanin biosynthesis, benzoxazinoid biosynthesis, and brassinosteroid biosynthesis, indicating that hosts regulate microbial communities through complex metabolic networks. Notably, genetic loci controlling microbial community structure underwent strong directional selection across eggplant subpopulations from different geographic origins, providing evidence for host–microbe coadaptive evolution. This study elucidates genetic regulatory patterns of eggplant rhizosphere microbiomes, enriching the theoretical framework of plant–microbe coevolution, with broad implications for microbiome-assisted crop improvement and sustainable agriculture.

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