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We describe new craniodental specimens of Litolophus gobiensis recently unearthed from the type locality of the genus, and conduct phylogenetic analyses of Eocene chalicotheres based on a data matrix containing 21 taxa and 58 craniodental characters. Although the phylogenetic relationships of the Eocene chalicotheres are not well resolved in the strict component consensus tree, the 50% majority rule consensus shows that two post–earliest Eocene chalicothere lineages are present. The first lineage represents the main line of chalicothere evolution, including “Grangeria” anarsius, Eomoropus, and post-Eocene chalicotheres. The second lineage, consisting of Litolophus gobiensis and Grangeria canina, is the sister group and stem member to the main lineage. The derivative strict reduced consensus tree, with three unstable taxa pruned, supports some tree topologies of the 50% majority consensus. The taxonomy of some chalicothere taxa is revised based on the phylogenetic analyses, such as “Grangeria” anarsius being probably better referred to the genus Eomoropus as originally identified, E. ulterior being the sister taxon to E. amarorum, and Lophiodon being excluded from the Ancylopoda but allied with the Ceratomorpha.