I've seen many photos of animals at the zoo, some are absolutely fantastic photos, some are something that you should cast in the trash bin. What is the secret behind those fantastic photos? Well, first off you should know that you want to portray the animal in as natural a scene as possible, I've not seen many photos that are good where the animal is obviously in a zoo (whether by a fence or otherwise). It should always be your first priority to find a way to make it look like the animal is not in a zoo or enclosed area.
Now you may be wondering how to do that, and here's the answer. First is to get a
good telephoto lens, a telephoto lens can significantly blur the fencing and/or wiring that is separating you from the animal. The amount of blur is determined by the focal length, how close you are to the fence/wire, and amount of aperture blades among other things. So, if executed correctly you can completely blur out the fence/wire, you may or may not be surprised that the following shot was take through wiring

. With my Canon 70-200 /4L positioned very close to the wiring, wide open aperture, and subject's distance a fair bit from my position I was able to make the wire cease to exist.
With this you must also realize what you can and cannot do. If the animal is pacing right next to fence then there is almost no way to eliminate all remnants of the fence from the image unless you have something like a Canon 200mm /1.8L or something to that extent. It is simply not possible to eliminate the fence when the subject is that close to it without the use of some super-aperture telephoto beast, and with that it will be extremely hard to lock on focus with very little to no room for error.
Next, you should execute the following technique: find the light. Repeat it after me, find the light, find the light, find the light. With this in mind, you should realize that it will be near impossible to photograph a very dark exhibit with very restrictive fencing such as might be found for birds in some zoos (aviaries not included). That is unless you have a powerful flash, but personally I'd be hesitant to use it. I don't believe it is right to use powerful strobes close to animals because you don't know how sensitive their eyes are or how they will respond to it, it could be dangerous for them to be near bright sources of light.
A well light exhibit with the subject a good distance from the fence will be your best bet for a great photo, also aviaries offer very good opportunities for photography as there are no fences separating you from your subject. Although another problem becomes more apparent with aviaries, and that is the fence behind the subject becomes a problem. This can destroy even some of the best photographs. You can mitigate the problem by using your lens on it's widest aperture, although even then if the bird flies to the top of the aviary it cannot be avoided sometimes. Your best bet with this is to buy a good quality telephoto lens with a very wide aperture or a long focal length telephoto, I'd recommend the Canon 70-200mm /2.8, Canon 200mm /2.8 or Canon 300mm /4 or better for this. I personally have been able to get by with a Canon 70-200 /4L, although I will be upgrading to the /2.8L as soon as I financially can.
Now with that taken care of we can move onto the next most essential thing to a successful zoo shot; composition. Most people compose the image with the subject in the center of the frame, however that is one of the least interesting compositions and thus not very successful. Take note of the rule of thirds, imagine a tic-tac-toe board across your image which divides it into 9 equal parts, the four points at which the lines intersect are the points of interest. The further you go away from those 4 points of interest the less interesting the subject gets, the closer the subject gets to the "danger zone", or edge of the photograph the more uncomfortable the viewer gets. (Sometimes it makes it interesting to get the viewer uncomfortable, and causes a good photo to become great, other times it destroys an image, so use good judgement on this) Of course rules can be broken, and the rule of thirds composition may not be the best for the image, but it is always good to keep in mind when composing an image. You ever been in a situation where you have very little time to compose an image and have to make a decision fast? Well, then that would be a good time to resort to the rule of thirds as it can be a lifesaver.
I have one final subject for this topic and that is image sharpness. This is almost always the first or last thing that defines a good image, the vast majority of the time you'll want your image to be "tack sharp" and if it isn't then the image is considered bad. This is where good quality lenses come into play, your autofocus/manual focus needs to be perfect when you take the image. You know how I said that you should use your lens at it's widest aperture when taking zoo shots? That also means that you have very little room for error when it comes to focus. Some things that I always do when taking zoo shots are setting the autofocus to only use the center point (find out how for your camera), focusing on the
eye (Of the utmost importance, the eye determines the overall sharpness of the image), and focusing again on the eye after every shot (sans when I am using burst mode). I'll say this again, the eye of the animal will determine how sharp the photo is, if everything but the eye is in focus then the shot is not in focus. And with that I hope I got you wanting to go to the zoo and taking some pictures

Quick recap:
1) To eliminate the fence/wire get as close as you can to it, use a wide aperture, and make sure your subject is a fair distance away from you.
2) Find good lighting for your subject and your picture will be vastly improved.
3) Get a good lens.
4) Remember compositional rules to help improve the composition of your shots and break rules to give an interesting effect.
5) Use the center autofocus point and a fast aperture lens to get the sharpest pictures.
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Thanks for the info!
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I am good at times with zoo photography, depending on the zoo though. But this helps
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