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I'm in with the Saint Louis Zoo. Not quite on par with San Diego, but it is free.
San Diego is the best Zoo, but it is very expensive. I also really like the Bronx Zoo and Pittsburgh Zoo.
Aquariums: Of the ones I have been to I like the National Aquarium in Baltimore. The Aquarium of the Pacific is nice, but relatively small. I really want to see the one in Atlanta.
If you're in San Diego for the Zoo, also visit the Wild Animal Park. has some zoo-like exhibits, and some expansive, open habitats where animals like giraffes and gazelles run around doing their own thing.
Monterey Aquariam in California - Awesome!!!! Baltimore aquariam - National Zoo - plus it,s free - and it you are not to tired or staying more than one day - you have the free Smithsonian, national monuments, etc
I like the often overlooked San Francisco Zoo. I think it's not as popular as it might have been because it has to compete with many other world class attractions in the city and the area. It is tucked away in a not very popular and rather rainy/cold corner of the city. Despite all that I think it's really quite good.
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