Molecular data have greatly influenced our concepts of species and their relationships in the last few decades, and as a consequence the taxonomy of most vertebrate clades has been repeatedly revised to reflect phylogeny. However, as larger and more complete molecular data sets become available, the sometimes striking disparities between taxonomic revisions based on individual gene trees (particularly those based on mitochondrial DNA) and species trees has become increasingly apparent. Here, we present data from 13 nuclear and one mitochondrial gene. Our results demonstrate that the recent taxonomic proposal erecting the new Australian chelid genus Flaviemys (Testudines: Chelidae) was an unnecessary action, and that recognition of Flaviemys confuses, rather than clarifies, a phylogeny-based taxonomy of the group. Taxonomic actions have many broad repercussions, and we recommend that taxonomic changes should be proposed cautiously and only when they are based on the strongest possible data and analyses.