Abstract Empirical data sets of intraspecific restriction site polymorphism in Drosophila have been gathered in order to test hypotheses derived from coalescent theory. Three main ideas are tested: (1) haplotype frequency in the sample contains information on the topological position of a given haplotype in a cladogram, (2) the frequency of a haplotype is related to the number of mutational connections to other haplotypes in the cladogram and (3) geographic location can be used to infer topological positioning of haplotypes in a cladogram. These relationships can then be used to better estimate intraspecific phylogenies in two ways: (1) rooting the phylogeny and (2) resolving ambiguities in a cladogram. This information will allow one to reduce the number of alternative phylogenies and incorporate the uncertainties involved in reconstructing intraspecific phylogenies into subsequent analyses that depend heavily on the topology of the tree.