Animal mitochondrial genomes usually have two transfer RNAs for leucine: one, with anticodon UAG, translates the four-codon family CUN, while the other, with anticodon UAA, translates the two-codon family UUR. These two genes must differ at the third anticodon position, but in some species the genes differ at many additional sites, indicating that these genes have been independent for a long time. Duplication and deletion of genes in mitochondrial genomes occur frequently during the evolution of the Metazoa. If a tRNA-Leu gene were duplicated and a substitution occurred in the anticodon, this would effectively turn one type of tRNA into the other. The original copy of the second tRNA type might then be lost by a deletion elsewhere in the genome. There are several groups of species in which the two tRNA-Leu genes occur next to one another (or very close) on the genome, which suggests that tandem duplication has occurred. Here we use RNA-specific phylogenetic methods to determine evolutionary trees for both genes. We present evidence that the process of duplication, anticodon mutation, and deletion of tRNA-Leu genes has occurred at least five times during the evolution of the metazoa-once in the common ancestor of all protostomes, once in the common ancestor of echinoderms and hemichordates, once in the hermit crab, and twice independently in mollusks.