Our recent studies on Potanichthys [1] and Wushaichthys [2] from China shed new light on the evolutionary origin and reproductive strategy of the Thoracopteridae. Tintori commented on our taxonomic assignment of Wushaichthys and on our hypotheses of gradual evolution of over-water gliding adaption and internal fertilization of thoracopterids [3][4][5]. Moreover, he questioned the provenance and age of Potanichthys [1] and Wushaichthys [2], and claimed that Potanichthys xingyiensis was a younger synonym of Thoracopterus wushaensis [5]. However, we do not agree with him on these points because Tintori's commentary is not based on a phylogenetic analysis and lacks supportive evidence.The taxonomy should be based on the results of phylogenetic analysis, not the reverse. Our phylogenetic studies [2] indicate that the traditional, poorly defined family Peltopleuridae is paraphyletic; the previously alleged 'peltopleurid' Peripeltopleurus [6] and the recently described Wushaichthys [2] are more closely related to four-winged thoracopterids than to Peltopleurus because they possess ambiguous features of Thoracopteridae. We have summarized five synapomorphies of Thoracopteridae in our recent contribution [2], and Wushaichthys is recovered as the most basal member of this family (figure 1a). The diagnosis of Wushaichthys starts from 'a basal thoracopterid distinguished from others of this family ' [2, p. 2]. That means the genus should first possess five synapomorphies of Thoracopteridae. The additional features listed in the diagnosis are enough to distinguish Wushaichthys from others of this family. Additionally, our phylogenetic studies suggest that Potanichthys [1] and Gigantopterus [3] are more derived than Thoracopterus [3] in having an almost naked body, median and fused premaxillae, and more than one supraorbitals. Thus, Potanichthys and Gigantopterus are not synonyms of Thoracopterus.Uniformitarianism, the concept that the present is the key to the past, has been recognized as a principle of geology and virtually all fields of science [7]. Under this concept, the differentiation of phenotypic traits in thoracopterids and peltopleurids has been interpreted as sexual dimorphism; those individuals with hooklets (claws) on the anal fin are supposed males and those without hooklets females [2,6]. Analogous to that in modern viviparous teleosts [8], the specialized anal fin in supposed males of thoracopterids and peltopleurids might function as a gonopodium and play an important role in sperm transfer, and consequently indicate a reproductive strategy of internal fertilization in these extinct taxa. Tintori's interpretation [5] of those thoracopterid individuals with hooklets on anal fin as females contrasts the condition observed in living fishes and, therefore, violates the concept of uniformitarianism, and his comment on our hypothesis of internal fertilization in thoracopterids lacks the support of evidence.