Two haplotypes were found for the S7 ribosomal protein gene intron, which differed by a G/A base. Some individuals were heterozygous, as evidenced by a double bump in the chromatogram. C. cognatus individuals from Antes Creek or from New York had exclusively the S7 haplotype with the G. Cave specimens with C. cognatus mitochondrial haplotypes could be homozygous or heterozygous for both S7 haplotypes. Likewise, cave specimens with C. bairdii mitochondrial haplotypes could also be homozygous or heterozygous for both S7 haplotypes. Thus, there is no correlation between nuclear haplotypes and mitochondrial clades, suggesting introgression within the cave population as a single reproductive unit. The Loose Tooth cave specimen was one of the specimens that had C. bairdii haplotype and an A, and the other specimen had C. cognatus haplotype and a G.