Palumbi et al. (2001) proposed a “three-times rule” that uses mitochondrial DNA (mtDNA) sequences to predict probabilities of monophyly for nuclear loci (i.e., whether the alleles within a taxon coalesce with one another before they coalesce with alleles from a sister taxon). They use neutral coalescent theory to infer these probabilities from the ratio of interspecific divergence to intraspecific variation of mtDNA. We show that the estimated probabilities have very wide confidence intervals because of the inherent stochasticity of the mtDNA coalescent process. Under neutrality, the true probability of monophyly can be much higher, or much lower, than predicted by the three-times rule. We also review recent empirical and theoretical studies that refute neutrality-based predictions concerning mtDNA variation and divergence. We conclude that the three-times rule is neither a useful test for neutral molecular evolution nor a reliable guide to genealogical species.