The zoo aquarium is the main zoo in madrid and very well worth the visit. (A great collection with giant pandas, iberian ibex, iberean red deer, lots of bears, dolphins, koalas, etc. But most exhibits are pretty standard)
The second park i visited was Faunia (
Faunia.es ), which is more themed, but it has not as many species as the zoo does (also not all the obvious zoo animals like elephants, lions/tigers, giraffes etc.). But still a couple of very interesting species (Mazama deer, manatees, lots of rare penguins (at least rare in zoos), a huge nocturnalhouse, etc.) However i didn't spend a lot of time there and i liked the zoo aquarium much better.
These 2 i've visited, but i know there is a safaripark somewhere around madrid, and i've read about a small zoo somewhere which sounded a bit obscure (sorry forgot the name)