Ueno Zoo (恩賜上野動物園) is the oldest Zoo in Japan, built in 1882. The zoo offers about 464 species off all kind of animals, sea creatures and birds. There are many restaurants and vending machines in the park to enjoy some refreshments. You can also take a short ride by Monorail to the south west area of the Zoo. In this area you can enjoy the Petting Zoo and other, more common animals. There is also a Reptile and Amphibian House and a Small Mammal House.
The zoo is closed on Monday, but is open from Tuesday to Sunday from 9:30 to 17:00 (tickets sold until 16:00). The admission fee is 600 yen for adult and free for kids (0-12). Ueno Zoo is located inside Ueno Park, which is just a short walk from Ueno station.
Official website (in English): http://www.tokyo-zoo.net/english/ueno/