The medaka, Oryzias latipes, is a model organism in experimental biology. Its ontogeny and osteology have been studied frequently, but no detailed description of its cranial anatomy exists. Based on manual dissections, histological slide sections, and 3D-reconstructions, we describe the anatomy of the jaw apparatus of O. latipes, focusing on musculature, connective tissue elements, and the nervous system. The soft tissue anatomy of the head of O. latipes is characterized by several derived characters that seem to be related to the modification of the upper jaw and a reduced mobility of its bones, which is an evolutionary novelty of the Beloniformes. These apomorphies could also be influenced by the small size of O. latipes. The maxilla is medial to the premaxilla. The presence of extensive connective tissue elements severely limits the mobility of both bones against each other and against the neurocranium. The external section of m. adductor mandibulae is partly fused with the internal section, originates from the quadrate, and inserts to the lower jaw. The intermediate head of the internal section is narrow and forms a bend along the ventral margin of the orbit. The intramandibular section is a separate narrow muscle between retroarcticular and dentary. These characters need to be verified in other representatives of Beloniformes to test their contribution to the disputed phylogenetic relationships within this taxon and to improve the understanding of the evolution of beak-like jaws in beloniform fishes.