Studies of the evolutionary history of gene families can provide important insight into the processes leading to functional conservation or divergence among orthologs and paralogs. While the pattern of relationships among family members may be difficult to predict prior to an analysis, there are several expectations that should be met that can provide evolutionary verifications for gene isolation and characterization studies. In this report, it is shown that a recently described jasmonic acid caboxyl methyltransferase (JMT) sequence from Capsicum annuum L. (hot pepper) fails to satisfy several evolutionary predictions. Specifically, the hot pepper sequence is more closely related to some Arabidopsis thaliana (L.) Heynh. strains than are other strains of A. thaliana or its close relative Brassica campestris L. In addition, the level of divergence of hot pepper and A. thaliana JMT is more than ten times lower than expected from the levels of divergence of their mitochondrial and plastid sequences. Finally, attempts to PCR amplify JMT from hot pepper DNA were unsuccessful. In light of these empirical results, the identity of the putative hot pepper JMT sequence is called into question and highlights the need for phylogenetic perspectives even for functional studies.