Despite the genetic tractability of many of Drosophila species, the genus has few examples of the “classic” type of hybrid zone, in which the ranges of two species overlap with a gradual transition from one species to another through an area where hybrids are produced. Here we describe a classic hybrid zone in Drosophila that involves two sister species, Drosophila yakuba and D. santomea, on the island of São Tomé. Our transect of this zone has yielded several surprising and anomalous findings. First, we detected the presence of an additional hybrid zone largely outside the range of both parental species. This phenomenon is, to our knowledge, unique among animals. Second, the genetic analysis using diagnostic molecular markers of the flies collected in this anomalous hybrid zone indicates that nearly all hybrid males are F₁s that carry the D. santomea X chromosome. This F₁ genotype is much more difficult to produce in the laboratory compared to the genotype from the reciprocal cross, showing that sexual isolation as seen in the laboratory is insufficient to explain the genotypes of hybrids found in the wild. Third, there is a puzzling absence of hybrid females. We suggest several tentative explanations for the anomalies associated with this hybrid zone, but for the present they remain a mystery.