A previous analysis of molecular phylogenies suggested that intraspecific diversification had occurred more recently in temperate-zone Northern Hemisphere reptiles and amphibians than in Southern Hemisphere taxa. Here, we test potential explanations for this pattern. We examined published phylogenetic analyses, derived from genetic sequence data, to generate two estimates of the age of species: (i) the oldest intraspecific diversification event within each taxon and (ii) the inferred timing of the split between two sister species. The timing of splits between species shows the same pattern as splits within species, and thus may be due to climatically driven cladogenic and extinction events or may be an artefact of differing levels of taxonomic knowledge about the fauna. Current rates of species descriptions suggest that many more taxa remain to be described in the Southern Hemisphere than the Northern Hemisphere; for that bias to fully explain our results on species age differences, the proportion of undescribed Southern taxa would need to be ≥ 12% in reptiles and ≥ 51% in anurans. For reptiles, taxonomic ignorance plausibly explains the apparent difference in mean age of species between the Southern and Northern Hemispheres; but this explanation can apply to amphibians only if a vast number of Southern taxa remain to be described.