Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.Chromosome inversions play an important role in local adaptation and speciation1,2, and selectively important inversions have been identified in many species3,4. Selection due to different environmental factors or stages in the life cycle1 may favour inversions carrying locally adapted alleles at several loci. In addition, established inversions are predicted to accumulate selectively important genetic differences, which may contribute to reproductive isolation during speciation1.Although few studies have identified the actual loci that influence selection on inversions2,4,5, rearrangements may be favoured due to gene alterations near breakpoints6, chromatin changes7 or combinations of advantageous, co-adapted alleles8. Inversions suppress recombination, so locally advantageous alleles may segregate together, causing higher fitness than recombinant haplotypes9. Most evolutionary studies have focused on widespread, older inversions, so we have little knowledge of the evolutionary processes that guide their initial increase in frequency. For example, do inversions drift to higher frequency, and then acquire new advantageous mutations after they are common? Or are multiple linked, advantageous alleles captured in a new inversion, allowing them to spread together? Analysis of younger inversions may elucidate the evolutionary forces controlling the initial spread of chromosome inversions, which therefore influence their role in adaptation and speciation4,8.Related species often differ for chromosome inversions that carry locally favoured alleles at multiple loci10,11. A key distinction among models for the evolution of inversions is whether early frequency increase is due to genetic drift or natural selection. Genetic drift might predominate initially, with subsequent accumulation of advantageous variants12. Alternatively, the Kirkpatrick–Barton model9 argues that linked, locally adapted alleles exist first, and subsequently are captured within a new, selectively favoured inversion13. In this ‘inversion-late’ evolutionary sequence1,5, linked quantitative trait loci (QTLs), similar to the ancestral haplotype that gave rise to the inversion, may still exist in non-inverted genotypes9. Here, we test these predictions of the Kirkpatrick–Barton model. First, we introduce ecologically diverged subspecies of Boechera stricta. Next, we examine a young inversion to infer the selective forces controlling its early increase in frequency. Finally, we cross collinear, standard genotypes from the hybrid zone to ask whether old, linked QTLs can be found within the inversion region.