Hybridization is an important feature of the evolution of many plant and an
imal groups. On one hand, it can be viewed as a natural experiment that pro
vides a window on evolutionary processes. On the other hand, it is a signif
icant evolutionary process in its own right that can lead to the origin or
merger of species. This chapter reviews the contributions of molecular appr
oaches to our understanding of hybrid zone structure and dynamics, phylogeo
graphy, reproductive isolation, introgression, and hybrid speciation. After
concepts and terminology are clarified, the potential utility of different
kinds of molecular markers for investigating hybridization is reviewed. Th
is is followed by an examination of several models that predict the structu
re and dynamics of hybrid zones and an exploration of empirical and theoret
ical studies that test the validity of these models. Finally, I will review
how molecular markers have informed our understanding of several consequen
ces of hybridization, such as introgression, hybrid speciation, species ext
inction, and phylogenetic incongruence.