Regions where related species’ ranges overlap have the potential to become zones of hybridization and also have the potential to reveal the progression of speciation between those species. The evolutionary history and genetic barriers to reproduction can be revealed by the pattern of ancestry across the genomes of hybrid individuals. Ancestry junctions, historical recombination events between chromosomes of different ancestries, can be used as a measure of ancestry. However, empirical identification of these junctions is rarely performed. Combining whole genome sequencing with probabilistic inference of ancestry, we have identified ancestry junctions across the genome of a single hybrid individual from the well-studied house mouse hybrid zone between Mus musculus musculus and Mus musculus domesticus in Central Europe. We found that the average block length between junctions was small, but the variance in block length was high. These results show a complex history of hybridization, and may reveal that hybridization has been occurring in the zone longer than previously thought. This analysis demonstrates the power of genomic data in increasing our understanding of speciation.