The effect of utilizing secondary structure on multiple alignment and phylogeny reconstruction was examined for the mitochondrial 12S ribosomal RNA and valine transfer RNA genes in the lizard family Opluridae. Computer-generated multiple alignments were performed under parsimony using gap costs of 1-10 both with and without reference to secondary structure. Alignments performed without secondary structure resulted in disruption of positional homology in some stems at all gap costs. Number of misaligned stem positions increased with gap cost. Phylogenetic analyses of multiple alignments without secondary structure recovered a well-supported morphological tree for five gap costs, and this was the single most parsimonious tree only for a gap cost of 1. Computer-generated multiple alignments using secondary structure to maintain positional homologs in stems recovered the morphological tree over all gap costs, and this was the single most parsimonious tree for 8 of 10 gap costs. The combined morphological and molecular data produced a single most parsimonious oplurid tree that was congruent with the morphological tree over all gap costs. Chalaradon madagascariensis is the sister taxon of Oplurus, which itself contains two clades: one with the arboreal Oplurus cuvieri and Oplurus cyclurus and the other with the saxicolous Oplurus grandidieri, Oplurus fierinensis, Oplurus quadrimaculatus, and Oplurus saxicola.