Previous studies on trait variation and sexual dimorphism in the dioecious plant Silene latifolia have shown genetic correlations among traits and differences between male and female G matrices, suggesting between-sex differences in the genetic architecture of traits. In order to describe the genetic basis of these traits, and to unveil the causes of the quantitative-genetic differences between the sexes, a QTL analysis was performed for 47 traits in a backcross derived from two artificial selection lines. In addition to many minor QTL expressed in both sexes, there were two types of sex-specific loci (some with major effect): those that cosegregated with the sex-determining region for all 40 sexually dimorphic traits, and those that mapped to the autosomes or pseudoautosomes for a limited number of traits. Traits known to be functionally related, or genetically correlated, often had co-occurring or colocalized QTL, whose polarity was in the expected direction. Moreover, QTL with the expected polarity based on the direction of selection had larger allelic substitution effects than QTL with contrary polarity. More QTL segregated and co-occurred in males than females, which agrees with previous findings of greater trait integration in males. Lastly, traits with different genetic correlations within the sexes were disproportionately represented by sex-specific QTL. These results show that between-sex differences in QTL patterns are congruent with differences based on quantitative-genetic results and with theory on the resolution of sexual conflict. They also agree with the hypothesis that trade-offs and trait integration are likely to affect males more than females.