Wildlife researchers primarily track fish using radio or satilite transmitters (aka tags), or in the case of marine mammals, freeze branding.
The size of the transmitter determines the method used for inserting it. Some transmitters are small enough to use a needle with (very similar to those pet-id chips which are inserted subcutaniously between the shoulder blades) and are placed intradermially. Sharks I know are given larger transmitters that are placed in the abdominal cavity through a surgical incision. Sharks may also be tagged on the dorsal or pectoral fin, but these tags are prone to being ripped out, thus lost, so I don't think this method is used any more. Look up shark research done on Bimini Island, Bahamas, they would have more reliable shark tagging methods.
Marine mammals such as dolphins are tagged with transmitters on the dorsal fin, as well as being freeze branded with an ID number just beneath the base of the dorsal fin. Transmitters and tags on the dorsal fin are prone to being ripped out, so they are usually only applied to one member of a certain pod. Dolphins are also photo IDed by the shape of their dorsal fin and the pattern of marks upon it. This method is not the most reliable because a dolphin's dorsal may change over time (aquire new markings, heal, etc), many dolphins may have a similar pattern of markings (aka tips removed, double notches, etc), and the perspective of the photo can make even the same dolphin look like two different individuals between takes. Seals I believe are tagged on their flukes or flippers, and may even be ID with a non-toxic paint applied to the skin, which of course will wear off over time. Notching the flipper may also be another possible method of seal ID.
Polar bears are sometimes ID using non-toxic spray paint as well as a radio collar. During the course of a project, bears are given number ID on their rumps for easy tracking by air. This paint wears off of course and leaves no perminate mark on the bear.
Freeze branding is a harmless proceedure. The brand is chilled with liquid nitrogen, then applied to the skin. Animals don't even flinch. Freeze brands are also used to ID wild mustangs for release, usually on the neck beneath the mane.
I am not aware of any method of painting fish for identification in the wild. It would not be a fast enough method since it would require taking the animal from the field to apply the dye. Dying wild fish would also not be suitable because, well, how does one see the dye marks when the fish is submerged? It would also change the color of that fish, making it "different" from the rest of the school and easier for a predator to pick off, in which case, your project is screwed.
~~Colesea
