PREMISE OF THE STUDY: Hybrid zones provide ‘natural laboratories’ for understanding the processes of selection, reinforcement and speciation. We sought to gain insight into the degree of introgression and the extent of ecological/phenotypic intermediacy in the natural hybrid strawberry, Fragaria × ananassa subsp. cuneifolia. METHODS: We used whole plastome sequencing to identify parental species-specific (Fragaria chiloensis and F. virginiana) chloroplast SNPs, and combined the use of these with nuclear microsatellite markers to genetically characterize the hybrid zone. We assessed the potential role of selection in the observed geographic patterns by bioclimatically characterizing the niche of the hybrid populations and phenotypically characterizing hybrid individuals of known genomic constitution. KEY RESULTS: Significant admixture and little overall maternal bias in chloroplast or nuclear genomes suggest a high degree of inter-fertility among the parental and hybrid species and point to a long history of backcrossing and genetic mixing in the hybrid zone. Even though hybrids were phenotypically intermediate to the parental species there was still a discernible fingerprint of the parental genotype within hybrid individuals. Thus, while the pattern of introgression observed suggests geographic limitations to gene flow, it may be reinforced by selection for specific parental traits in the bioclimatically-intermediate habitat occupied by the hybrid. CONCLUSION: This work uncovered the genetic complexity underlying the hybrid zone of the wild relatives of the cultivated strawberry. It lays the foundation for experimental dissection of the causes of genomic introgression and nuclear-cytoplasmic disassociation, and understanding other parts of the Fragaria evolutionary history.