AbstractThe South American and West Indian Casque‐headed Treefrogs (Hylidae: Hylinae: Lophyohylini) include 85 species. These are notably diverse in morphology (e.g. disparate levels of cranial hyperossification) and life history (e.g. different reproductive modes, chemical defences), have a wide distribution, and occupy habitats from the tropical rainforests to semiarid scrubland. In this paper, we present a phylogenetic analysis of this hylid tribe based on sequence fragments of up to five mitochondrial (12S,16S,ND1,COI,Cytb) and six nuclear genes (POMC,RAG‐1,RHOD,SIAH,TNS3,TYR). We included most of its species (> 96%), in addition to a number of new species. Our results indicate: (i) the paraphyly ofTrachycephaluswith respect toAparasphenodon venezolanus; (ii) the nonmonophyly ofAparasphenodon, withArgenteohyla siemersi,Corythomantis galeataandNyctimantis rugicepsnested within it, andAp. venezolanusnested withinTrachycephalus; (iii) the polyphyly ofCorythomantis; (iv) the nonmonophyly of the recognized species groups ofPhyllodytes; and (v) a pervasive low support for the deep relationships among the major clades of Lophyohylini, includingC. greeningiand the monotypic generaItapotihylaandPhytotriades. To remedy the nonmonophyly ofAparasphenodon,Corythomantis, andTrachycephalus, we redefinedNyctimantisto includeAparasphenodon(with the exception ofAp. venezolanus, which we transferred toTrachycephalus),Argenteohyla, andC. galeata. Additionally, our results indicate the need for taxonomic work in the following clades: (i)Trachycephalus dibernardoiandTr. imitatrix; (ii)Tr. atlas,Tr. mambaiensisandTr. nigromaculatus; and (iii)Phyllodytes. On the basis of our phylogenetic results, we analyzed the evolution of skull hyperossification and reproductive biology, with emphasis on the multiple independent origins of phytotelm breeding, in the context of Anura. We also analyzed the inter‐related aspects of chemical defences, venom delivery, phragmotic behaviour, co‐ossification, and prevention of evaporative water loss.