Reproductive barriers between sister species of the mushroom-forming fungi tend to be stronger in sympatry, leading to speculation on whether they are being reinforced by selection against hybrids. We have used population genomic analyses together with in vitro crosses of a global sample of the wood decay fungus Trichaptum abietinum to investigate reproductive barriers within this species complex and the processes that have shaped them. Our phylogeographic analyses show that T. abietinum is delimited into six major genetic groups: one in Asia, two in Europe, and three in North America. The groups present in Europe are interfertile and admixed, whereas our crosses show that the North American groups are reproductively isolated. In Asia, a more complex pattern appears, with partial intersterility between subgroups that likely originated independently and more recently than the reproductive barriers in North America. We found pre-mating barriers in T. abietinum to be moderately correlated with genomic divergence, whereas mean growth reduction of the mated hybrids showed a strong correlation with increasing genomic divergence. Genome-wide association analyses identified candidate genes with programmed cell death annotations, which are known to be involved in intersterility in distantly related fungi, although their link here remains unproven. Our demographic modeling and phylogenetic network analyses fit a scenario where reproductive barriers in Trichaptum abietinum could have been reinforced upon secondary contact between groups that diverged in allopatry during the Pleistocene glacial cycles. Our combination of experimental and genomic approaches demonstrates how T. abietinum is a tractable system for studying speciation mechanisms.