Hemiphractids have a singular mode of reproduction that involves maternal care. The Andean‐endemic Gastrotheca marsupiata species group includes direct‐developing and tadpole‐bearing species, the latter trait being unique among Gastrotheca. Larval morphology has proven to be a valuable source of evidence to understand the taxonomy and evolution of frogs but remains understudied in Hemiphractids. Herein, we redescribe the larval cranium of G. espeletia, G. gracilis, G. marsupiata, G. peruana, G. pseustes, and G. riobambae, and describe those of G. aureomaculata, G. chrysosticta, G. litonedis, G. monticola and G. psychrophila. Additionally, based on the data gathered, we explore their phylogenetic significance, expanding the knowledge regarding Gastrotheca larval internal morphology. We suggest that the presence of the posterolateral process of crista parotica, the concave palatoquadrate, the quadratoorbital commissure, and the proximal commissures II and III are putative synapomorphies for Gastrotheca. Furthermore, we suggest the long pseudopterygoid process as a putative synapomorphy for Hemiphractyidae.