Abundant representation of sharks in the fossil record makes this grou
p a superb system in which to investigate rates and patterns of molecu
lar evolution and to explore the strengths and weaknesses of phylogene
tic inferences from molecular data. In this report, the molecular evol
ution of the cytochrome b gene in sharks is described and the informat
ion related to results from phylogenetic analysis of the data evaluate
d in the light of a phylogeny derived independently of the molecular d
ata. Across divergent lineages of sharks there is evidence for signifi
cant substitution rate variation, departure from compositional equilib
rium, and substantial homoplasy; nevertheless, the signal of evolution
ary history is evident in patterns of shared transversions and amino a
cid replacements.