AbstractLittle is known about the embryonic development and variation of the chondrocranium in Crocodylia and there are no works on any Caiman species. Due to the importance of cranial features in the systematics of this clade, investigating the development of the skull in embryonic stages is essential. In this study, we present for the first time the development of the cartilaginous skull of two extant Caiman species. Anatomical descriptions of the embryonic chondrocranium of Caiman latirostris and Caiman yacare were made, paying special attention to their inter‐ and intraspecific variation. For this purpose, pre‐hatching ontogenetic cranial series of these two caiman species were prepared with a double staining and diaphanization technique. The main differences with other crocodylian species were observed in the palatoquadrate, and interspecific variation within the genus was recorded in the hyobranchial apparatus and larynx. Some characters may be distinctive of Caiman (posterior and ventral surface of the otic process of the palatoquadrate articulated with the dorsal process of the columella auris, and otic process articulated with the lateral wall of the auditory capsule), Alligatoridae (presence of an epiphanial foramen) or C. latirostris and C. yacare (Corpus hyoidei with different number and position of foramina and different shapes of its anterior contour and anterior and posterior notch, different degrees of broadening of the distal end of the Cornu branchiale I, and presence/absence of a notch in the posteroventral surface of the cricoid). Homologies of the elements belonging to the hyobranchial apparatus could not be confirmed. As in other tetrapods the trachea consists of incomplete cartilaginous rings. Morphological changes and dissimilarities found in this study are useful as a context to start studying phylogenetic constraints. Moreover, in a heterochronic context, variations may be involved.