Although separated by millions of years of evolutionary history, most fish and reptiles are vertebrates who share a number of similar traits, including the presence of a vertebral columns and scales, as well as ectothermic metabolisms. However, as both groups are very speciose, numerous exceptions exist.
Both reptiles and fish are vertebrates, and most species possess a series of bones that enclose and protect their spinal cord. Some groups, such as the sharks and rays, have replaced bone with cartilage over their evolutionary history, but they are still firmly nested within the vertebrate family tree.
Another characteristic common to all vertebrates is the presence of a central nervous system, comprised of a brain and network of nerves. These nerves control movement of the animal and relay information about the external world to the animal's brain. All living vertebrates also possess a number of other common characteristics, including the presence of gills at some point in their lives. However, while fish retain their gills throughout their lives, reptiles lose their gills while they are still in the embryonic stage.
Most reptiles and fish bear scaly outer coverings, although exceptions exist in both categories. For example, catfish have no external scales and snakes occasionally exhibit a genetic mutation in which they fail to produce scales. Scientists hypothesize that scales provide a number of advantages to the animals who bear them, including protection and increased speeds.
However, fish scales and reptile scales are not homologous -- meaning that they do not arise from the same embryonic tissues. Fish have scales that arise from dermal -- bony -- tissue and have a somewhat similar composition to bone. Turtles and crocodilians also possess dermal scales, but they arise via a different process. Snakes and lizards bear keratinized scales, which form from within the epidermis, or skin tissue.
As a reminder of their evolutionary history, birds, which are phylogenetically part of the reptile family tree, also bear scales on their feet. These scales form from the epidermis, somewhat like those of snakes and lizards do.
Most reptiles and fish are ectothermic, or "cold-blooded," animals, which means that their body temperature fluctuates with that of the environment. To raise their body temperature, many reptiles must bask in the sun; fish are rarely able to thermoregulate in this method, courtesy of the homogeneous nature of their habitat. Instead, they must alter their behavior to match the ambient temperature, rather than to manipulate their internal temperature. In general, ectothermic animals exhibit higher activity levels, eat more and grow more quickly at higher temperatures, while they become lethargic and cease feeding at lower temperatures.
Exceptions to this general trend exist. Leatherback sea turtles (Dermochelys coriacea), for example, have a low surface to volume ratio and thick layer of fat, which insulates them very well. Accordingly, they often maintain body temperatures above that of the surrounding water. Additionally, some fish, such as moonfish (Lampris guttatus), tuna (Thunnus spp.) and mackerel sharks (Lamnidae) exhibit adaptations that allow them to maintain elevated body temperatures.