The paucity of fungal species known to be currently hybridizing has significantly hindered our understanding of the mechanisms driving gene introgression in these eukaryotic microbes. Here, we describe an area of hybridization and gene introgression between the invasive plant pathogen Heterobasidion irregulare (introduced from North America) and the native H. annosum in Italy. A STRUCTURE analysis of amplified fragment length polymorphism data for 267 individuals identified gene introgression in 8–42% of genotypes in the invasion area, depending on site. Data indicate that introgression is mostly occurring unilaterally from the native to the invasive species and is responsible for 5–45% of genomes in admixed individuals. Sequence analysis of 11 randomly selected and unlinked loci for 30 individuals identified introgression at every locus, thus confirming interspecific gene flow involves a large number of loci. In 37 cases, we documented movement of entire alleles between the two species, but in 7 cases, we also documented the creation of new alleles through intralocus recombination. Sequence analysis did not identify enrichment of either transcriptionally different nonsynonymous alleles or of transcriptionally identical synonymous alleles. These findings may suggest introgression is occurring randomly for extant alleles without an obvious enrichment process driven by selection. However, further studies are needed to ensure selection is not at work elsewhere in the genome.