Recent studies have identified pathogenic variants in the FOXI3 gene associated with craniofacial microsomia pedigrees. In zebrafish, the foxi1 gene is considered a functional homolog of the mouse Foxi3. However, research on foxi3a and foxi3b, which display homologous genes in the naming of FOXI3 in zebrafish, has predominantly focused on their roles in epidermal ionocyte function. Our study reveals that disruption of foxi3a or foxi3b results in a reduced number of cranial neural crest cells (CNCCs) and hypoplastic mandibular cartilage in zebrafish. These findings introduce a new perspective on the functional homologs of FOXI3 and highlight an unrecognized role of foxi3 in zebrafish CNCC and mandibular development.