Despite the typical assumption in studies of mitochondrial diversity that such data are useful for approximating population size and demography, studies of sequence diversity in mitochondrial DNA across the Metazoa have shown a surprising excess of rare alleles, a pattern associated either with strong selection or population growth. Previous work has shown that this bias toward an excess of rare alleles is typical across the Crustacea, and in particular, in the Cirripedia (barnacles). Here, we directly evaluate sequence data from studies of barnacle populations to ensure that inclusion of cryptic species is not the cause of this pattern. The results shown here reinforce previous studies that suggest caution in interpreting such patterns of allele frequencies, as they are likely to be influenced both by demographic changes and selection.