Rarest animals seen in a zoo or aquarium

I know sea otters are kept at the Lisbon Oceanarium. I saw those in 2018 (first and only time).
 
Rare for the world:
- Nervous Whaler Shark (Reef HQ)
- Urogymnus dalyensis (Cairns Aquarium)
- Spotted Handfish (Melbourne Aquarium)
- Giant Cuttlefish (Melbourne Aquarium)
- Ebinania brephocephala (Osaka Aquarium)
- Japanese Lates (Osaka Aquarium)
- Spinetail Mobula Ray (Osaka Aquarium)
- Whitecheek Shark (Tokyo Sea Life Park)
- Leaping Blenny (Tokyo Sea Life Park)
- Striped Boarfish (Tokyo Sea Life Park)
- Bluefin Tuna (Tokyo Sea Life Park)
- Nurseryfish (Tokyo Sea Life Park)
- Duck-Billed Platypus (Sydney Aquarium)
- Dugong (Sydney Aquarium)

Rare for the country the aquarium/zoo is in:
- Redtail Catfish (Mooloolaba Aquarium)
- Black Pacu (Mooloolaba Aquarium)
- Giant Gourami (Mooloolaba Aquarium)
- Giant Pangasius (Mooloolaba Aquarium)
- Emerald Tree Monitor (Cairns Aquarium)
 
Leaping Blenny (Tokyo Sea Life Park)

Monterey Bay Aquarium has some of these, whether the same species or not I don't know.

Redtail Catfish (Mooloolaba Aquarium)
- Black Pacu (Mooloolaba Aquarium)
- Giant Gourami (Mooloolaba Aquarium)
- Giant Pangasius (Mooloolaba Aquarium)

Funny to see these as rare, as I have seen them all offered in the aquarium trade somewhat regularly! (Some other Pangasius at least, and I think Giant)
 
Monterey Bay Aquarium has some of these, whether the same species or not I don't know.
I don't know which species MBA has but the ones I saw were Alticus saliens.

Funny to see these as rare, as I have seen them all offered in the aquarium trade somewhat regularly! (Some other Pangasius at least, and I think Giant)
Quite a few of the large exotic freshwater fish are pretty hard to come by in Australia, I believe it's the quarantine laws that make it difficult to import animals. Giant Gourami are occasionally found in pet stores but they are usually in a display tank/pets of the owner, and not for sale. The only aquarium that I know of in Australia that has a large collection of large exotic freshwater fish was Mooloolaba Aquarium, but they have since been replaced with Little Penguins.
 
One very rare species I have seen is the Chaco eagle (Buteogallus coronatus).
Only two individuals are held captive in the world, one in Les Aigles du Léman, in Sciez - France, where I saw it, the other one in the zoo of the Universidade Federal de Mato Grosso. The species is considered Endangered, with a very small widl population making it rare both in captivity and in the wild.
 
Ive really only seen one super rare species, but here are some rare species I’ve seen.

In the world:
.Hawaiian monk seal

In my home country:
.chinese goral
.sunda slow loris
.transcaspian urial
.Persian goitered gazelle
.sommerings gazelle
.Daurian pika
.shoebill storks
.crowned eagle
.kagu
.tuatara
And probably more rare birds at sdz.
 
- Dugong
- Baja California Pronghorn
- Quokka
- Ghost Bat
- Ornate Hawk-Eagle
- Great Frigatebird
- Red-Footed Booby
- Superb Lyrebird
- Kagu
- Satin Bowerbird
- Sociable Weaver
- Masked Butterflyfish
- Hawaiian Cleaner Wrasse
- Bay Ghost Shrimp
- Kamehameha Butterfly
 
- Dugong
- Baja California Pronghorn
- Quokka
- Ghost Bat
- Ornate Hawk-Eagle
- Great Frigatebird
- Red-Footed Booby
- Superb Lyrebird
- Kagu
- Satin Bowerbird
- Sociable Weaver
- Masked Butterflyfish
- Hawaiian Cleaner Wrasse
- Bay Ghost Shrimp
- Kamehameha Butterfly
Where did you see the Red-Footed booby?
 
Lesser mouse-deer (Tragulus kanchil) - Singapore Zoo & Night Safari
Spix's macaw - Jurong Bird Park (Singapore) [The exhibit was closed when I last went as I went quite late in the evening but they're there!]
Dugong - Underwater World (Singapore, while the park still operated)
Okapi - Berlin Zoo

And while I don't think this counts as a zoo, but I think one of the rarest animals in the world that I've seen is the Takahē at the Te Anau Bird Sanctuary in New Zealand! A lot bigger than I imagined and very, very gorgeous colours!

These are just a few animals I consider to be rare in captivity :-)
 
For now keeping it to mammals, may or may not do other animals later.
Bush dog(Zoo Atlanta)
Raccoon dog (Zoo Atlanta)
Giant panda (Zoo Atlanta)
Blue duiker (Birmingham Zoo)
Lowland anoa (Zoo Miami)
Banteng (don't know if these are rare in zoos, but haven't heard about them being seen much; Zoo Miami)
Giant eland (Zoo Miami)
Red-flanked duiker (Birmingham Zoo)
Babirusa (DAK, Jacksonville Zoo)
Visayan warty pig (Jacksonville Zoo)
Eld's deer (DAK)
Four-striped grass mouse (DAK)
Southern pudu (Jacksonville Zoo)
New Guinea singing dog (Zoo Miami)
Dhole (Zoo Miami)
Black-footed cat (Birmingham Zoo)
African wild cat (Birmingham Zoo)
Black duiker (Zoo Miami)
Red wolf (Chewhaw Zoo)
Collared lemur (DAK)
Coquerel's sifaka (correct me if these aren't rare either, or with anything on the list actually; Jacksonville Zoo)
Drill (Zoo Atlanta)
Lion-tailed macaque (DAK)
Grant's gazelle (Zoo Miami)
Green monkey (Wild Adventures)
Patas monkey (Wild Adventures)
Guanco (Zoo Miami)
Indian crested porcupine (Wild Adventures)
Gerenuk (Zoo Miami)
Vampire bat (Jacksonville Zoo)
Seba's short-tailed fruit bat (Jacksonville Zoo)
Arabian oryx (Zoo Miami)
Dwarf mongoose (Birmingham Zoo)
Walrus (SeaWorld Orlando)
Slender-horned gazelle (Zoo Miami)
Addra gazelle (Zoo Miami)
Blackbuck (DAK, Lion Country Safari, Wild Adventures)
Nilgai (Lion Country Safari)
Okapi (DAK, Miami, Jacksonville)
Prehensile-tailed porcupine (Chattanooga Zoo)
White-lipped peccary (Zoo Miami)
 
For now keeping it to mammals, may or may not do other animals later.
Bush dog(Zoo Atlanta)
Raccoon dog (Zoo Atlanta)
Giant panda (Zoo Atlanta)
Blue duiker (Birmingham Zoo)
Lowland anoa (Zoo Miami)
Banteng (don't know if these are rare in zoos, but haven't heard about them being seen much; Zoo Miami)
Giant eland (Zoo Miami)
Red-flanked duiker (Birmingham Zoo)
Babirusa (DAK, Jacksonville Zoo)
Visayan warty pig (Jacksonville Zoo)
Eld's deer (DAK)
Four-striped grass mouse (DAK)
Southern pudu (Jacksonville Zoo)
New Guinea singing dog (Zoo Miami)
Dhole (Zoo Miami)
Black-footed cat (Birmingham Zoo)
African wild cat (Birmingham Zoo)
Black duiker (Zoo Miami)
Red wolf (Chewhaw Zoo)
Collared lemur (DAK)
Coquerel's sifaka (correct me if these aren't rare either, or with anything on the list actually; Jacksonville Zoo)
Drill (Zoo Atlanta)
Lion-tailed macaque (DAK)
Grant's gazelle (Zoo Miami)
Green monkey (Wild Adventures)
Patas monkey (Wild Adventures)
Guanco (Zoo Miami)
Indian crested porcupine (Wild Adventures)
Gerenuk (Zoo Miami)
Vampire bat (Jacksonville Zoo)
Seba's short-tailed fruit bat (Jacksonville Zoo)
Arabian oryx (Zoo Miami)
Dwarf mongoose (Birmingham Zoo)
Walrus (SeaWorld Orlando)
Slender-horned gazelle (Zoo Miami)
Addra gazelle (Zoo Miami)
Blackbuck (DAK, Lion Country Safari, Wild Adventures)
Nilgai (Lion Country Safari)
Okapi (DAK, Miami, Jacksonville)
Prehensile-tailed porcupine (Chattanooga Zoo)
White-lipped peccary (Zoo Miami)

Some of these are fairly rare, others not so much. Babirusa, Visayan Warty Pig, Pudu, Red Wolf, Coquerel's Sifaka, Patas Monkey, Guanaco, Gerenuk, Dwarf Mongoose, Blackbuck, Nilgai, Okapi, and Prehensile-tailed Porcupine aren't really rare. A few others I don't think are either.
 
Are bush dogs that rare in the US? I don’t think they’re that common in Europe but nothing too notable
 
Seba's short-tailed fruit bat (Jacksonville Zoo)

Hate to break it to you, but this species is far from rare :p it's one of the most widely held species of bat in the country, and definitely the most numerous.

Vampire bats are held in 15 or 16 places in the US, so not too rare either.

Some of the other species you have (other than those @Great Argus listed) are rare in the States though - among those Drill, Raccoon Dog, Giant Eland, Walrus, White-lipped Peccary, Green Monkey, Dhole, and African Wild Cat.
 
Hate to break it to you, but this species is far from rare :p it's one of the most widely held species of bat in the country, and definitely the most numerous.

Vampire bats are held in 15 or 16 places in the US, so not too rare either.

Some of the other species you have (other than those @Great Argus listed) are rare in the States though - among those Drill, Raccoon Dog, Giant Eland, Walrus, White-lipped Peccary, Green Monkey, Dhole, and African Wild Cat.
To be honest, my visit to Jacksonville that day was the first time I heard of Seba's short tail, so I assumed it was rare. Also thought an animal that would feast on blood wouldn't be too popular, so there's that assumption.
 
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