Recent methodological advances permit a rigorous comparison of phylogenetic trees for hosts and their parasites to determine the extent to which these groups have cospeciated through evolutionary time. In cases where significant levels of cospeciation are indicated, comparison of amounts of evolutionary change that have accumulated along analogous branches in the host and parasite trees provides a direct assessment of relative rates of evolution in the two groups. For such a comparison to be meaningful, the features compared in the hosts and parasites should be genetically based, evolutionarily homologous, and should evolve in a roughly time-dependent fashion within each group. Nucleotide sequences encoding homologous genes in hosts and parasites are an ideal source of data for comparative studies of evolutionary rates. Recent studies of pocket gophers and their lice are used to illustrate the variety of questions that can be addressed through phylogenetic study of host-parasite systems.