A gene is imprinted when its level of expression is dependent on the sex of the parent it was inherited from. An unusual consequence of imprinting is that male and female additive genetic variances differ, and so ignoring imprinting can lead to misspecification of a number of evolutionary parameters, including the predicted response to selection. QST - the differentiation of quantitative traits between populations - is a consequence of the combined effects of both neutral and selective forces acting across the metapopulation. QST is often compared to FST, the differentiation across populations measured at (presumably) neutral loci, in order to determine the role of selection in shaping trait divergence between populations. Previous theoretical work has demonstrated that properties of the genetic basis of a quantitative trait, such as inbreeding, dominance and epistasis, can marginally inflate or deflate QST, although it is unlikely that any of these properties would be strong enough to “hide” the effects of strong selection. Here, we assess the effects of imprinting on QST by exploring a two-population model of migration, inbreeding, selection and imprinting. We show that imprinting is unlikely to hide the effects of divergent selection, lending further support to the general conclusion that strong selection is unlikely to be masked by inter- and intra-locus interactions. However, the magnitude of imprinting’s effect on QST is surprisingly large – ignoring imprinting, and hence the differences between male and female additive genetic variances, will lead to considerable over-estimation of the strength of selection.