In this study four mitochondrial genes (cytochrome oxidase I, ATPase, cytochrome b, control region) were amplified from most of the fish species found in the freshwaters of south-eastern Queensland, Australia. The performance of these different gene regions were compared in terms of their ability to cluster fish families together in a neighbour-joining tree, both individually by gene and in all combinations. The relative divergence rates of each of these genes were also calculated. The three coding genes (cytochrome oxidase I, ATPase, cytochrome b) recovered similar numbers of families and had broadly similar divergence rates. ATPase diverged a little more quickly than cytochrome oxidase I, and cytochrome b slightly more slowly than cytochrome oxidase I. All two gene combinations recovered the same number of families. Results from the control region were much more variable, which, although generally possessing more diversity than the other regions, was often less variable.