Most bony fishes have two sets of jaws made mainly of bone. The primary oral jaws open and close the mouth, and a second set of pharyngeal jaws are positioned at the back of the throat. The oral jaws are used to capture and manipulate prey by biting and crushing. The pharyngeal jaws, so-called because they are positioned within the pharynx, are used to further process the food and move it from the mouth to the stomach.

Cartilaginous fishes, such as sharks and rays, have one set of oral jaws made mainly of cartilage. They do not have pharyngeal jaws. Generally jaws are articulated and oppose vertically, comprising an upper jaw and a lower jaw and can bear numerous ordered teeth. Cartilaginous fishes grow multiple sets (polyphyodont) and replace teeth as they wear by moving new teeth laterally from the medial jaw surface in a conveyor-belt fashion. Teeth are replaced multiple times also in most bony fishes, but unlike cartilaginous fishes, the new tooth erupts only after the old one has fallen out.

Jaws probably originated in the pharyngeal arches supporting the gills of jawless fish. The earliest jaws appeared in now extinct placoderms and spiny sharks during the Silurian, about 430 million years ago. The original selective advantage offered by the jaw was probably not related to feeding, but to increased respiration efficiency—the jaws were used in the buccal pump to pump water across the gills. The familiar use of jaws for feeding would then have developed as a secondary function before becoming the primary function in many vertebrates. All vertebrate jaws, including the human jaw, evolved from early fish jaws. The appearance of the early vertebrate jaw has been described as "perhaps the most profound and radical evolutionary step in the vertebrate history". Fish without jaws had more difficulty surviving than fish with jaws, and most jawless fish became extinct.

Jaws use linkage mechanisms. These linkages can be especially common and complex in the head of bony fishes, such as wrasses, which have evolved many specialized feeding mechanisms. Especially advanced are the linkage mechanisms of jaw protrusion. For suction feeding a system of linked four-bar linkages is responsible for the coordinated opening of the mouth and the three-dimensional expansion of the buccal cavity. The four-bar linkage is also responsible for protrusion of the premaxilla, leading to three main four-bar linkage systems to generally describe the lateral and anterior expansion of the buccal cavity in fishes. The most thorough overview of the different types of linkages in animals has been provided by M. Muller, who also designed a new classification system, which is especially well suited for biological systems.

The skull of fishes is formed from a series of loosely connected bones. Lampreys and sharks only possess a cartilaginous endocranium, with both the upper and lower jaws being separate elements. Bony fishes have additional dermal bone, forming a more or less coherent skull roof in lungfish and holost fish.

The simpler structure is found in jawless fish, in which the cranium is represented by a trough-like basket of cartilaginous elements only partially enclosing the brain, and associated with the capsules for the inner ears and the single nostril.

Cartilaginous fish, such as sharks, also have simple skulls. The cranium is a single structure forming a case around the brain, enclosing the lower surface and the sides, but always at least partially open at the top as a large fontanelle. The most anterior part of the cranium includes a forward plate of cartilage, the rostrum, and capsules to enclose the olfactory organs. Behind these are the orbits, and then an additional pair of capsules enclosing the structure of the inner ear. Finally, the skull tapers towards the rear, where the foramen magnum lies immediately above a single condyle, articulating with the first vertebra. There are, in addition, at various points throughout the cranium, smaller foramina for the cranial nerves. The jaws consist of separate hoops of cartilage, almost always distinct from the cranium proper.

In ray-finned fishes, there has also been considerable modification from the primitive pattern. The roof of the skull is generally well formed, and although the exact relationship of its bones to those of tetrapods is unclear, they are usually given similar names for convenience. Other elements of the skull, however, may be reduced; there is little cheek region behind the enlarged orbits, and little, if any bone in between them. The upper jaw is often formed largely from the premaxilla, with the maxilla itself located further back, and an additional bone, the symplectic, linking the jaw to the rest of the cranium.