About a year ago, I completed a search through all the species listed on ISIS. The top 10 species in each category are as follows:
MAMMALS: 1. House mouse 11,097; 2. Seba's short-tailed bat 9106; 3. Brown rat 5430;
4. Goat 5162; 5. Sheep 3792; 6. Red-necked wallaby 3010; 7. Fallow deer 2935; 8. Ring-tailed lemur 2501; 9. Jamaican fruit bat 2452; 10. Egyptian rousette bat 2434
BIRDS: 1. Budgerigar 7922; 2. Houbara bustard 5389; 3. American flamingo 4822; 4. Chilean flamingo 4807; 5. Greater flamingo 4662; 6. Common peafowl 3896; 7. Red jungle fowl 3570; 8. Mallard 2715; 9. Humboldt’s penguin 2624; 10. Zebra finch 2528
REPTILES AND AMPHIBIANS: 1. Kihansi spray frog 5070; 2. Common slider 4535; 3. Green and black poison frog 2553; 4. Oregon spotted frog 2017; 5. American alligator 1731; 6.
Blue poison dart frog 1607; 7. Houston toad 1443; 8. Yellow-banded poison dart frog 1402; 9. Mission golden-eyed tree frog 1247; 10. Boa constrictor 1244
FISHES: 1. Guppy 4,009,823; 2. Cardinal tetra13,635; 3. Goldfish 7547; 4. Common carp 7477; 5. Nile tilapia 7315; 6. Red piranha 5018; 7. White cloud mountain minnow 2525;
8. Glowlight tetra 2414; 9. Neon tetra 2358; 10. Scaled herring 2128
INVERTEBRATES: 1. Leafcutter ant 10,350,704; 2. Honeybee 409,815; 3. Madagascan hissing cockroach 75,103; 4. Three-colored hermit crab 16,487; 5. Clonal plumose anemone 12,875; 6. Strawberry false coral 12,355; 7. Red-lined cleaner shrimp 11,933;
8. Lightfoot snail 11,094; 9. Black boring sea urchin 10,287; 10. Sunburst diving beetle 10,284
There are quite a few surprises here, but I suspect many are due to a few zoos having large groups of some species, rather than some 'common' species being evenly distributed among collections. I can't tell if the house mice and brown rats include individuals destined to be fed to other animals. Some animals definitely seem to be over-represented, such as various domestic animals and the flamingoes. I have not included the 100,001 Amur tigers that suposedly exist in Seoul as I believe the figure is a typing error; otherwise the tiger would the fourth most abundant species in zoos (after the leafcutter ant, guppy and honeybee.
I compiled the lists using figures from species represented by at least 500 individuals, so I have additional data, if anyone is interested.