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Research on the molecular systematics of higher taxa in the butterfly family Nymphalidae (Lepidoptera) is only just beginning. Outgroup selection is difficult at the moment due to the lack of consensus on the basal relationships of the major groups in Nymphalidae. We identify four major clades in the Nymphalidae based on a cladistic analysis of one mitochondrial gene sequence (COI, 1450bp) and two nuclear gene sequences (EF-1α, 1064bp, and wingless, 412–415bp) from 54 exemplar species sampled from all currently recognized subfamilies. The COI data set was found to be highly incongruent with the nuclear data sets and a Partitioned Bremer Support analysis shows that the COI data set largely undermines support for most clades. Transitions at the third codon positions of the COI data set were highly saturated, but analyzing the combined data set with the COI third positions removed did not change the …