Abstract. Coalescence theory predicts when genetic drift at nuclear loci will result in fixation of sequence differences to produce monophyletic gene trees. However, the theory is difficult to apply to particular taxa because it hinges on genetically effective population size, which is generally unknown. Neutral theory also predicts that evolution of monophyly will be four times slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. Variation in mitochondrial DNA (mtDNA) within and between species has been studied extensively, but can these mtDNA data be used to predict coalescence in nuclear loci? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The ''three-times rule'' states that, on average, most nuclear loci will be monophyletic when the branch length leading to the mtDNA sequences of a species is three times longer than the average mtDNA sequence diversity observed within that species.A test using mitochondrial and nuclear intron data from seven species of whales and dolphins suggests general agreement with predictions of the three-times rule. We define the coalescence ratio as the mitochondrial branch length for a species divided by intraspecific mtDNA diversity. We show that species with high coalescence ratios show nuclear monophyly, whereas species with low ratios have polyphyletic nuclear gene trees. As expected, species with intermediate coalescence ratios show a variety of patterns. Especially at very high or low coalescence ratios, the threetimes rule predicts nuclear gene patterns that can help detect the action of selection. The three-times rule may be useful as an empirical benchmark for evaluating evolutionary processes occurring at multiple loci. The application of molecular sequence data to systematics, population biology, and forensic identification of species often depends on whether monophyly has evolved at particular loci between taxa (Hudson 1992;Moritz 1994;Moore 1995;Palumbi and Cipriano 1998). Monophyly of genes is basic to some views of the species concept (Baum and Shaw 1995) and has been used to define evolutionarily significant units for management of threatened species (Moritz 1994). A population that has been separate long enough to develop gene monophyly has probably developed novel combinations of alleles at many genetic loci and may possess unique evolutionary features including adaptation to local environment that should be considered by resource managers (Moritz 1994). The shape of intra-and interspecific gene trees has also been used to infer the demographic history of species (Takahata 1995) and speciation patterns (M. P. Hare, F. Cipriano, and S. Palumbi, unpubl. ms.). Monophyly is also important if molecular tools are used in the identification of managed species in commercial markets (whales: Baker et al. 1993;Cipriano and Palumbi 1999; seals: Malik et al. 1997; canned fish: Rehbein et al. 1997; cannabis: Jagadish et al. 1996; caviar: Cohen 1997). This is...