One of the most startling discoveries in avian molecular phylogenetics is that the volant tinamous are embedded in the flightless ratites, but this topology remains controversial because recent morphological phylogenies place tinamous as the closest relative of a monophyletic ratite clade. Here, we integrate new phylogenomic sequences from 1,448 nuclear DNA loci totalling almost one million base pairs from the extinct little bush moa, Chilean tinamou and emu with available sequences from ostrich, elegant crested tinamou, four neognaths and the green anole. Phylogenetic analysis using standard homogeneous models and heterogeneous models robust to common topological artefacts recovered compelling support for ratite paraphyly with the little bush moa closest to tinamous within ratites. Ratite paraphyly was further corroborated by eight independent CR1 retroposon insertions. Analysis of morphological characters reinterpreted on a 27-gene paleognath topology indicates that many characters are convergent in the ratites, probably as the result of adaptation to a cursorial life style.