Abstract The systematics of gomphotheres in South America is confused, and the status of some taxa is still subject to discussion. Recently, Prado and Alberdi published a cladistic analysis of the trilophodont gomphotheres, with emphasis on the South American species. Unfortunately, the paper has problems in many points, which invalidates the phylogeny itself and the biogeographic analysis of Alberdi et al. based on it. This paper reviews the problems of the analysis of Prado and Alberdi. The main problems of their analysis are: poor taxon sampling, exclusion of non-South American species of genera present in South America, inadequate choice of outgroup, use of outdated software and methodology, and several mistakes in coding of characters. Rebuilding of the original character matrix and analysis using TNT software resulted in a new consensus tree from five equally parsimonious trees. In the analysis, Rhynchotherium , Sinomastodon , Gnathabelodon , Eubelodon and a clade containing the three South American taxa form a polytomy that have Gomphotherium as a sister group. Sinomastodon and Gnathabelodon were successive branches toward the South American taxa in Prado and Alberdi’s result. The main point of this contribution is to correct the errors in the original analysis and character coding, including polymorphism when necessary, and to use updated software and weighting strategy. The result is much less resolved than that of Prado and Alberdi, but is has a strong influence on the conclusions that those authors drew from the original phylogeny and the biogeographic implication presented in Alberdi et al.