[Objectives]  To construct a new morphological index system for the Aphodiinae (Coleoptera: Scarabaeidae), the adults of which are very similar in external morphology complicate accurate classification into genera and tribes. Previous studies have shown that the morphology of the epipharynx can effectively distinguish some species, but it was not known whether the same criteria could be used to identify higher taxa. [Methods]  818 species belonging to 276 genera were used as research samples, including 799 species, 259 genera and 7 tribes of the Aphodiinae, and 19 species and 17 genera as outgroup samples (13 genera and 14 species of the Scarabaeinae, 4 genera and 5 species of the Aegialiinae). Morphological information on the epipharynx was quantified by means of geometric morphometrics. The ability of this information to classify species to the generic and tribal levels was then evaluated, and the morphology of the ancestors of the Aphodiinae was reconstructed using cladistic methods based on epipharyngeal morphology. [Results]  Based on Principal Component Analysis, the total morphological variation at the genus and at tribal levels was estimated to be 0.032 131 27 and 0.03 291 463, respectively. The degree of epipharyngeal variation among genera and tribes was small (about 3%), which reveals that epipharyngeal morphology has remained basically stable in the higher-level taxa. In order to determine whether the epipharynx is more similar among higher taxa, we also performed a discriminant function analysis. The results showed that 98.49% of genera and 98.41% of tribes can be correctly identified on the basis of epipharyngeal differences, which suggests that, although epipharyngeal differences are slightly better at discriminating genera than tribes, they are generally suitable for the discrimination and classification of the higher taxa of the Aphodiinae. Combined with a phylogenetic tree, the reconstructed ancestral shape of the epipharynx suggests that it has six variable morphological features, including the base, the lateral margin of the epitorma, the corypha and the shape of the epipharyngeal marginal. [Conclusion]  The results validate the previous use of some epipharyngeal features to resolve the taxonomy of the Aphodiinae, and also has identified some new morphological indexes. The epipharyngeal features are suitable for the classification of Aphodiinae into genera and tribes using quantitative morphology, and this approach has provided a new paradigm for resolving the taxonomy of groups with a high degree of external morphological convergence.