The main idea between the Conservation Centers for Species Survival concept is to have large numbers of a species present in one location, often in one or several herds, for ease of introductions, breeding, and social management. The challenge that can result is telling the members of those herds apart. Genetic and demographic management of a population requires a keeper to know who is who in their herd, and that can be a mite tricky when you're dealing with, say, thirty antelope in a pasture.
Ideally, there would be enough variation between individuals - a twisted horn, a peculiar marking, a difference in size - that a keeper would be able to know their animals easily by sight. And that does happen... when you're a conventional zoo and your "herd" consists of three or four individuals. When dealing with larger numbers (especially in large enclosures), different steps might be taken.
One solution is to ear tag your animals, each tag having a number and possibly using different color combinations. Males can be tagged in the right ear, females in the left. It sounds simply... and it generally is. Still, ear tags can fall off, and they can be difficult to read from a distance (a reason that it may be ideal to rely on color rather than just number). Many zoo professionals find themselves shying away from these, mostly because of aesthetic. It can be hard to convince your visitors of the majesty and rarity of your exotic ungulates when they look like a bunch of Bessie's, grazing ear-tagged in a field.
Other options include tattooing, freeze-branding, and ear-notching. In the later, a series of small notches are made in the ears of the antelope or deer (ears are large, erect, and often visible), with the sequence of notches representing different numbers. The process should inflict no pain or damage to the animal's ear, being comparable to a human having his or her ears pierced.
The fanciest, most high tech methods is microchipping animals. Like most fancy, high tech methods, I find it to be the one that works the least. For one thing, you can't read the chip from a distance. Secondly, the damn things always seem to move under the skin, meaning that they are never where they are supposed to be, and you spend forever searching for increasingly irate animal with a scanner, hoping to hear that tell-tale "beep.
All of these methods are also used in various combinations to study animals in the field, if any reminder was needed that the management of animals in zoos and in the wild is becoming increasingly blurred. Many hoofstock keepers I know, even those at the C2S2 facilities, are still able to identify their animals as individuals at a quick glance. For records and for confirmation, however, especially during moves between facilities, sometimes a more intrusive approach is needed.