Phylogenetic placement of most species of darters is reasonably well understood regarding their closest relatives. However, an exception is the apparently extinct Etheostoma sellare. In this paper, we included E. sellare in a phylogenetic analysis with 62 extant species representing one or more species from all previously recognized darter subgenera. The analysis included 77 new, or previously proposed, polarized, morphological characters for E. sellare and those characters plus reported molecular sequences (RAG1) for the extant species. A parsimony analysis of concatenated data for each species produced nodes congruent with the subgeneric taxonomy of darters and established unambiguous placement for the morphologically distinctive E. sellare placed in the newly created subgenus Mooreichthys to resolve a previous triotomy in which the single taxon was grouped with subgenera Poecilichthys and Litocara. Unique morphological or nucleotide synapomorphies support the monophyly of the subfamily Etheostomatinae and the most basal genus Percina sister to sister genera Ammocrypta and Etheostoma. Other unique synapomorphies support relationships within genus Percina, a close relationship of subgenus Allohistium to a clade containing subgenera Etheostoma Ulocentra Nanostoma, rather than to subgenus Nothonotus, and the monophyly of subgenus Catonotus. Relationships of some species, including sisters E. mariae and E. parvipinne, remain uncertain.