Sliding window analysis of the nucleotide alignment of all available Taenia mtDNAs provided an indication of nucleotide diversity (π) within and between mitochondrial genes (Figure 2). The plot readily shows the high degree of nucleotide variation within and between genes amongst the aligned Taenia genomes for any given window of 300 bp (π ranges from 0.094 to 0.333), and the possibility that hitherto untested regions of mtDNAs may be of utility. GenBank holds relatively few mitochondrial markers for a few species of Taenia, used variously for population genetics and diagnostics, but include partial fragments of cox1, cytb [60,62], nad1 [63], rrnS and atp6 (unpublished data available on GenBank). Sliding window analysis (and computation of number of variable positions per unit length of gene), indicates that genes with high sequence variability included nad6 (0.517), nad5 (0.517), atp6 (0.490), nad3 (0.480) and nad2 (0.479). Genes with the lowest sequence variability (per unit length) include cox1 (0.296), cox2 (0.323) and rrnS (0.330). Sequence variability within genes appears to be highest, with notable peaks and troughs of π, in cox1, rrnS and nad5. A plot of the number of phylogenetically informative sites in the same alignment, and using the same sliding window parameters, revealed a very close correlation between sequence variability and phylogenetically informative sites (Figure 2), allowing π to be used as a readily available proxy for phylogenetic signal; DnaSP [64] calculates π easily, but the plot of phylogenetically informative positions is more tedious. Nucleotide variability within species tends to reflect the same pattern observed amongst closely related species (e.g. within a genus; Littlewood, unpublished). Combined, these results suggest alternative gene regions are worthy of consideration in developing new genetic markers for phylogenetics, population genetics and diagnostics. Current mt genes used as targets for multiplexed PCR-RFLP based approaches to diagnostics [20,21,65] include cox1 and cytb; cox1 is also a chosen target for a novel loop-mediated isothermal amplification method of diagnosis [66]. Although relatively easy to amplify routinely, cox1 is amongst the slowest evolving, and least variable of genes available in the entire mtDNA suggesting that more reliable, or at least more informative, markers should be considered for future work, especially diagnostics involving mixed infections or other Taenia species.