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Charaxinae (Lepidoptera: Nymphalidae) has a worldwide distribution, although it occurs mainly between the tropics. Most species occur in the Neotropics, where three tribes, Preponini, Anaeomorphini, and Anaenini, can be found. Collectively, these three tribes encompass 109 species. Because of its relevance to systematics and taxonomy, the male genitalia of Lepidoptera have been extensively studied. The male genitalia are composed of the last two abdominal segments and their modifications for mating, known as claspers of the bodies. In order to improve upon the systematic classification of the subfamily, 31 species of 13 genera of Neotropical Charaxinae were analyzed. All characters relevant to species and generic taxonomy were analyzed. Most structures showed morphological variations among tribes, genera, and species. These variations demonstrated to be important to Preponini, because the structural patterns of the genitalia allow the separation in two groups, Prepona Boisduval and Archaeoprepona Fruhstorfer, and are in accord with the recent taxonomic classification proposed by Ortiz-Acevado and Willmott (2013), wherein Agrias Doubleday is synonymized in Prepona and Noreppa Rydon within Archaeoprepona. In the same way, Anaeomorpha splendida Rothschild showed considerable differences from Preponini's genera, the tribe in which it was included, confirming the revalidation of the tribe Anaeomorphini (Ortiz-Acevado and Willmott 2013). Substantial variation was found in the genital structures of Anaeini, making it difficult to establish structural patterns for this group. Such structural variation, however, may be very efficient to diagnose species, such as some species of Memphis Hübner and Fountainea Rydon, which can be easily identified through the presence and location of spines on the valva.