Few studies have reported on the morphology of Malveae fruits; particularly scarce are those examining internal morphology. The fruits of Malveae are considered schizocarps, and inside the mericarps, they have an appendix termed as the endoglossum. This structure presents different degrees of prominence among genera of the tribe, ranging from vestigial to well-developed. Although the external morphology of the endoglossum in Gaya has been studied, few studies have described its anatomy and ontogeny, knowledge which would contribute to our understanding of the evolution of such structure in the context of Malveae. Therefore, we herein propose to establish the origin of the well-developed endoglossum based on the ontogenesis of fruits of two species of Gaya, G. domingensis Urb. and G. gaudichaudiana A.St.-Hil., as well as a description of its tissues. To accomplish this, the usual techniques in plant anatomy were used to produce permanent slides for optical microscopy and sample preparation for scanning electron microscopy. Based on these studies, it was determined that the endoglossum structure in Gaya species has mixed origin, one from the basal portion of the carpelar mesophyll and another from the internal carpel epidermis. It can be concluded that the endoglossum, as herein validated, is a useful character for systematic and phylogenetic analyses in Gaya.