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Women tend to choose partners who resemble their father in certain characteristics. In non-human mammals, similar parental imprinting-like effects are often odour-mediated1,2, which requires not only learning of parental odour but also similarity between parents and prospective mates in the microbial communities responsible for production of the critical volatile compounds. Here, in light of growing recognition of human capacity for social olfaction3,4, we tested the possibility that women’s preferences are shaped by paternal phenotype. Axillary body odour samples from women’s fathers and romantic male partners were evaluated for similarity at the perceptual level as well as in both their microbiome diversity (using 16S rDNA sequencing) and chemical composition (using GC×GC-TOFMS). We found that partners’ body odour was perceived as more similar to paternal odour than would be expected by chance. In parallel, similarities in both microbiota composition and chemical profiles were significantly higher in partner-father dyads than in randomly generated dyads. While women’s relationship quality with the father did not predict father-partner similarity in microbial or chemical profiles, it was positively associated with perceived odour similarity. Our results thus reveal a suite of mechanisms by which parental odour cues can serve as a template in human mate choice.