1) Baccharis × intermedia (Asteraceae), found in central Chile, is a naturally occurring hybrid derived from the parent species B. macraei and B. linearis. It represents an extraordinary example of admixture with additive plant chemistry; however, the genetic structure of the hybrid complex and its evolution are still unclear. 2) Intensive field sampling and Genotyping-by-Sequencing (GBS) was used to clarify the structure of the B. × intermedia hybrid complex. In addition, B. vernalis, another species that resembles the morphology of B. macraei, was subjected to analysis to ascertain its role in the hybridization process. 3) A total of 3724 SNPs and 378 individuals were analyzed using clustering, PCA, Treemix, Patterson’s D- and f-statistics. Furthermore, other genetic indicators, such as levels of heterozygosity, Tajima’s D and nucleotide diversity (π) also provided further insight into the hybrid complex. 4) Our results show that B. × intermedia consists of mainly F1-hybrids with 18 % backcrossing to both parental species. B. vernalis was not involved into recent hybridization with B. macraei and B. linearis. Additionally, a recent introgression into the Quintay population of B. macraei from B. linearis was detected during the analysis. 5) Altogether, our extensive field sampling combined with genetic analyses have provided deeper insights into the genetic structure and evolution of the B. × intermedia hybrid complex in Chile.

1) Baccharis × intermedia (Asteraceae), found in central Chile, is a naturally occurring hybrid derived from the parent species B. macraei and B. linearis. It represents an extraordinary example of admixture with additive plant chemistry; however, the genetic structure of the hybrid complex and its evolution are still unclear. 2) Intensive field sampling and Genotyping-by-Sequencing (GBS) was used to clarify the structure of the B. × intermedia hybrid complex. In addition, B. vernalis, another species that resembles the morphology of B. macraei, was subjected to analysis to ascertain its role in the hybridization process. 3) A total of 3724 SNPs and 378 individuals were analyzed using clustering, PCA, Treemix, Patterson’s D- and f-statistics. Furthermore, other genetic indicators, such as levels of heterozygosity, Tajima’s D and nucleotide diversity (π) also provided further insight into the hybrid complex. 4) Our results show that B. × intermedia consists of mainly F1-hybrids with 18 % backcrossing to both parental species. B. vernalis was not involved into recent hybridization with B. macraei and B. linearis. Additionally, a recent introgression into the Quintay population of B. macraei from B. linearis was detected during the analysis. 5) Altogether, our extensive field sampling combined with genetic analyses have provided deeper insights into the genetic structure and evolution of the B. × intermedia hybrid complex in Chile.