Two mechanisms have been suggested for why the races of hybrid zones should have diverged:

• The two forms diverge by parapatric speciation: that is, while they were geographically contiguous along an environmental gradient. The forms diverge almost to the point of being two species and the border between them is recognized as a primary contact hybrid zone.

• The two forms first diverged allopatrically; their ranges then changed, and they spread up to each other's borders. Prezygotic reproductive isolation, however, had not evolved, and they could interbreed and form hybrids. Hybrid zones are then cases of secondary contact: they exist because populations have diverged allopatrically and subsequently come back into contact.

Neither mechanism is theoretically controversial but there can be empirical controversy about any particular hybrid zones: it is difficult to tell whether the races of most hybrid zones diverged allopatrically or while in contact.