Photo Credit: russ
The world famous San Diego Zoo is located in Balboa Park, less than 5 minutes from downtown San Diego. It is centrally located, and very easy to get to, and also very worth it. Once you're on the grounds, it seems worlds away from southern California.
The zoo is world renowned, and you will see why once you visit. There are animals from habitats all over the world. For more information, visit the official zoo website.
If zoos and enclosures aren't your thing, you can always head up road to Escondido and visit the Wild Animal Park, where you can see animals in more natural surroundings. Most of the animals are in one huge enclosure which is many acres large, where they interact as they would in the wild. The experience is like a one hour safari, in which you take a tram around the grounds to see what the park has to offer.