Studies of gamete structure and fertilization biology have revealed much about the phylogeny of molluscs. Recent studies of fertilization in chitons support the view that the basal order of chitons, the Lepidopleurida, fertilize eggs, as most molluscs do, by fusing the entire sperm with the egg and transferring chromatin, mitochondria, and centrioles into the egg cytoplasm. However, current evidence suggests that all members of the order Chitonida inject only chromatin into the egg. These chitons, which include the controversial family Callochitonidae, share a series of synapomorphic characters based on their fertilization biology that makes them unique. Current evidence suggests that Callochitonidae are basal to this order and sister taxa to the remaining Chitonida, which have been divided into two suborders, the Chitonina and Acanthochitonina. New evidence indicates that Chitonina have at least two different mechanisms for penetrating the egg. One group of species has pores in the egg hull (e.g., Chaetopleura apiculata (Say in Conrad, 1834) and Stenosemus albus (Linnaeus, 1767), whereas a second group has a continuous dense layer on the surface of the egg hull that is digested by the sperm (e.g., Rhyssoplax tulipa (Quoy and Gaimard, 1835) and Stenoplax conspicua (Pilsbry, 1892)). However, the genus Ischnochiton Gray, 1847 appears to be polyphyletic, as several species have distinctive characters that typify other genera or families. In particular, this genus needs to be re-evaluated using modern morphological and molecular methods. All of the Chitonina have spiny-hulled eggs with narrow bases and are quite different from the second suborder, Acanthochitonina, which is characterized by large-hull cupules with wide bases. Within Acanthochitonina, some species have open-hull cupules, whereas most have closed ones. Open-cupule species lack micropores in the hull for sperm entry, whereas several closed-cupule species exhibit micropores between hull cupules. These features of the egg are accompanied by alterations in sperm structure, such as position of the mitochondria and structure of the basal body, acrosome, and flagellum. Knowledge of the gamete structure of individual species and their fertilization biology, as demonstrated here, provides a different series of characters that can help avoid mistakes that are inherent during early development of new methods, such as molecular analyses. New details of fertilization biology have made it possible to revise preliminary analyses and provide an updated phylogeny of chitons, which differs in some important respects from other recent publications.