Both: Dwarf mongoose; eastern ring-tailed vontsira; northern narrow-striped boky; Barbary lion; ring-tailed coati
Berlin
Meerkat
Arabian sand and Sri Lankan rusty-spotted cats; jaguarundi; ocelot; lion; north Persian leopard; jaguar
Fennec; African wild dog
Giant panda; Asiatic black, polar and Indian sloth bears
Asian small-clawed otter; tayra
California sea lion; Cape and northern fur seals
Eastern Atlantic harbour seal
Kinkajou
Plzen
Hausa genet; Philippine palm civet; Palawan binturong
Banded, yellow and common slender mongooses; dark cusimanse
Canadian lynx; bobcat; Missouri cougar; Sudan cheetah; Palawan leopard cat; snow leopard; Siberian tiger
East African bat-eared and Cape foxes; maned wolf; wolf; southern black-backed jackal
European brown bear
Eurasian otter
Nepalese red panda
Berlin has eared and true seals and has more species of mustelids, procyonids and bears; Plzen has civets and a red panda and has more species of dogs and mongooses
Berlin wins on families with more species.
Birds
Both: Greater rhea; common emu; Humboldt penguin; American white, pink-backed and Australian pelicans; western cattle egret; little bittern; Asian woolly-necked, marabou and European white storks; hamerkop; Madagascar crested ibis; Chilean and greater flamingos; crested screamer; fulvous, white-faced and West Indian whistling, mandarin, white-winged, Philippine, yellow-billed, North American wood and ferruginous ducks; northern and Chilean pintails; Argentine and northern shovelers; tufted pochard; Bernier’s, falcated, Hottentot and Eurasian green-winged teals; common eider; Chiloe and Eurasian wigeons; garganey; common goldeneye; rosy-billed, common and red-crested pochards; European greater scaup; ruddy shelduck; smew; bar-headed, Egyptian, emperor, Hawaiian, red-breasted and blue-winged geese; black and black-necked swans; Eurasian and hooded mergansers; king vulture; Northern Harris' hawk; bald and golden eagles; Western Eurasian griffon and hooded vultures; Palawan peacock and Edwards's pheasants; Malaysian great argus; Asian blue and harlequin quails; grey junglefowl; eastern grey-crowned, red-crowned and Indian sarus cranes; red-legged seriema; corncrake; common redshank; ruff; pied avocet; common ringed plover; masked lapwing; black-naped and orange-fronted fruit, Madagascar turtle, Namaqua, red-necked Sulawesi, ruddy and cinnamon ground doves; Luzon and Mindanao bleeding-hearts; Nicobar and wonga pigeons; European eagle owl; tawny frogmouth; hooded and turquoise parrots; kea; blue-naped mousebird; Guira cuckoo; blue-winged and laughing kookaburras; northern Carmine bee-eater; Visayan tarictic hornbill; greater yellow-naped woodpecker; red bishop; white-spectacled bulbul; pied crow; black-throated, Gouldian, masked, star and chestnut-eared finches; Cuban grassquit; chestnut-backed ground thrush; blue-faced honeyeater; white-backed magpie; Bali mynah; bearded parrotbill; tricolor parrotfinch; Java sparrow; Asian glossy, emerald, golden-breasted and Brahminy starlings; common waxbill; grey-headed social weaver; Kilimanjaro white-eye
Berlin in bold; Plzen in italics
South African ostrich; southern cassowary; Common ostrich
Northern brown kiwi
Elegant crested tinamou
Western rockhopper, jackass and king penguins
Dalmatian pelican; Eurasian great cormorant; great white and spot-billed pelicans
Abdim’s, Maguari and black storks; Southern boat-billed and Indian pond herons; black-faced, scarlet and Puna ibises; waldrapp; Eurasian Spoonbill; African open-billed and yellow-billed storks; black-crowned and Philippine rufous night, Javan pond, eastern purple, green-backed, grey, white-faced and goliath herons; little egret; African spoonbill; Australian white, glossy, Hadada, sacred, straw-necked and black-headed ibises
Lesser, Andean and James flamingos
Bahama pintail; bronze-winged, North American ruddy and Magellanic steamer ducks; South African pochard; red-shouldered and Sharp-winged teals; common shelduck; Greenland white-fronted, magpie, snow, swan and barnacle geese; bufflehead; Coscoroba and whooper swans; American, South African and Australian black, lesser, spotted, wandering and plumed whistling, flying steamer, freckled, Hawaiian, Maccoa, maned wood, Meller's, Muscovy, Old World comb, ruddy, Patagonian crested and Laysan ducks; Chinese and Indian spot-billed ducks; yellow-billed pintail; New Zealand shoveler; American green-winged, blue-winged, Cape, chestnut, cinnamon, marbled, red-billed, speckled, Sunda, versicolor and Baikal teals; American wigeon; Australian hardhead; lesser and New Zealand scaups; Australian, paradise and black-backed rajah shelducks; Baer’s pochard; Cape barren, lesser white-fronted, magpie, pink-footed, ruddy-headed and greylag geese; Bewick’s swan
African fish and bataleur eagles; Western Egyptian, bearded, white-headed and palm-nut vultures; Andean condor; crested caracara; American black and western turkey vultures; eastern red-tailed hawk;, white-tailed and Steller's sea and greater spotted eagles; American and European kestrels; European peregrine, saker and lanner falcons; gyrfalcon; striated caracara
Bare-faced and great curassows; blue-throated piping guan; crested wood partridge; Germain’s and grey peacock, Lady Amherst's and Elliot's pheasants; Malayan crested and Siamese fireback pheasants; red junglefowl; black and yellow-necked francolins; Natal Helmeted guineafowl; Australian brush turkey; Barbary Madagascar, white-necklaced and Cypriot Chukar partridges; white-crested kalij; Bianchi’s, Mikado, Sichuan, northern green, Persian, Salvadori's, Southern Caucasian, Vietnamese, Zarudny's, Zerafshan and Khivan pheasants; Korean, Manchurian, Mongolian, Taiwan and Chinese ring-necked pheasants; Indian peafowl; Cochin-chinese and Vietnamese red jungle fowl; black grouse; European, Jungle bush and Gambel's quails; Eastern crested guineafowl; Chaco chacalaca
East African white-bellied bustard; kagu; sunbittern; Black and spotted crakes; buff-banded and water rails; common moorhen; demoiselle, white-naped and sandhill cranes
African wattled and long-toed lapwings; ruddy turnstone; black-necked stilt; Eurasian curlew; inca tern; spotted dikkop; African grey-headed, black-tailed, grey, laughing, slender-billed and black-headed gulls; arctic tern; African three-banded, European golden and Egyptian plovers; blacksmith and southern lapwings; black-winged stilt; bush and European thick-knees; collared pratincole; common sandpiper; Eurasian oystercatcher
Coroneted and red-bellied fruit, crested quail, emerald, laughing and crested doves; green-naped pheasant-pigeon; rock pigeon; western orange-bellied fruit-dove; Ashy and common wood, pink, western crowned, western rock, Philippine metallic, pink-necked green, Madagascar blue and green, pied, stock and pink-headed pigeons; silver-tipped, spotted, Sunda green and chestnut-naped imperial pigeons; bar-shouldered, beautiful and superb fruit, white-eared brown, blue-headed wood, Cape, European, red, ruddy and eastern oriental turtle, Island collared, Chinese spotted, diamond, Indian emerald, Malay spotted-necked, peaceful, pink-breasted, Senegal laughing, Socorro, Stephan's, white-winged, zebra and barred doves
Blue-fronted, red-lored, white-fronted and Cuban amazons; mountain parakeet; blue-winged, hyacinth, Mexican green military, red-fronted and great green macaws; citron-crested, palm, red-tailed black, white and Major Mitchell's cockatoos; galah; coconut and Goldie's lorikeets; eclectus parrot; rose-headed parakeet; Tanimbar corella; Vernal hanging, black, Bourke’s, golden-shouldered, greater vasa, scarlet-chested, swift and blue-winged parrots; black-cheeked and Madagascar lovebirds; budgerigar; crimson, green, northern and eastern rosellas; Dammermann’s masked, yellow-fronted parakeet and red-fronted parakeets; green military macaw; iris, Mindanao, Mitchell's, scaly-breasted, Stella's, Sumba and marigold lorikeets; purple-naped lory; Port Lincoln ringneck; Philippine cockatoo
Common and northern white-faced scops, ferruginous pygmy, Eurasian great grey and spectacled owls; Ashy-faced, burrowing, Central European barn, Central European tawny, little, Philippine scops and boobook owls
Channel-billed cuckoo; greater roadrunner; Common cuckoo; Philippine koel
Black-faced and white-bellied go-away birds; violet and white-cheeked turacos; Senegal turaco
Kikuyu speckled and speckled mousebirds
White-fronted bee-eater; Abyssinian and southern ground, silvery-cheeked, Polillo, Von der Decken's and northern pied hornbills; blue-bellied and purple rollers; brown-hooded kingfisher; common hoopoe; Collared kingfisher; red-throated bee-eater; Javan rhinoceros, Southern Sulawesi tarictic, Palawan and Luzon hornbills
Bearded, red-and-yellow and D’Arnaud’s barbets; black-necked and pale-billed aracaris
Red avadavat; southern red bishop; scarlet-headed blackbird; western bluebill; Asian fairy bluebird; common, white-eared and red-whiskered bulbuls; red-rumped cacique; yellow-fronted canary; northern cardinal; white-eared catbird; blue-capped and red-cheeked cordon-bleus; spangled cotinga; cut-throat, long-tailed and double-banded finches; Uganda red-billed and vinaceous firefinches; long-tailed fiscal; blue grosbeak; white-crested laughing thrush; red-billed leiothrix; red-billed blue magpie; golden-headed manakin; trumpet manucode; chestnut-breasted munia; common and greater hill mynas; grey-headed oliveback; red-throated parrotfinch; red-winged pytilia; African quailfinch; white-necked raven; black-and-white seedeater; African silverbill; amethyst, greater blue-eared and Rueppell's glossy, Asian pied, wattled and superb starlings; copper sunbird; blue-grey, paradise and Brazilian tanagers; orange-headed and spotted palm thrushes; Dybowski's and Peters's twinspots; zebra waxbill; white-headed buffalo, speckle-fronted, Taveta golden and village weavers; Black-throated accentor; Indian red avadavat; Madagascar bilbfinch; fire-crowned and Napoleon bishops; blackcap; brush and common bronzewings; Asian black, chestnut, Chinese red-whiskered, cream-striped, eastern and western white-eared, Himalayan, Layard's, light-vented, red-vented, ruby-throated, Upper Guinea and black-headed bulbuls; northern bullfinch; central Asian rock, red-headed and house buntings; Island canary; African and common chaffinches; common crossbill; black-faced dacnis; fieldfare; plum-headed, red-billed and yellow-billed long-tailed, Timor zebra and trumpeter finches; diamond, red-browed and painted firetails; Madagascar fody; European goldfinch; blue-backed grassquit; European and oriental greenfinches; Chinese grosbeak; hawfinch; hypocolius; great kiskadee; Atlas horned, wood and black larks; black-throated, buffy, eastern moustached, red-fronted, red-tailed, red-winged, scaly, Siamese White-crested, spectacled, Sumatran and blue-crowned laughing thrushes; common linnet; Emei Shan liocichla; Asian and Iberian azure-winged and Maghreb magpies; chestnut-breasted and grand mannikins; black-faced, Indian scaly-breasted, Javan, white-headed, Malaysian chestnut, pale-headed and dusky munias; bank, golden-crested, pale-bellied, Sulawesi, yellow-faced and crested mynas; slender-billed spotted and spotted nutcrackers; Eurasian golden and Montserrat orioles; blue-faced and Fiji parrotfinches; redpoll; western black, common, Moussier's and Güldenstädt's redstarts; oriental magpie and rufous scrub robins; white-crowned robin-chat; long-tailed rosefinch; Siberian rubythroat; European serin; red-backed shrike; Eurasian siskin; eastern fox, Sudan golden and Timor sparrows; black-collared, European, Miombo blue-eared, purple glossy, purple-backed, rosy, scissor-billed, short-tailed, spotless, white-shouldered and coleto starlings; barn swallow; black-breasted, grey-backed, Japanese, mistle, Eurasian song and Siberian thrushes; azure, dark grey and coal tits; Sumatran treepie; grey and white wagtails; oriole warbler; Bohemain waxwing; western village weaver; black wheatear; chestnut-flanked white-eye; yellowhammer
Berlin has a kiwi and mousebirds; Plzen has a tinamou. While Plzen has far more species of birds in practically all categories, Berlin wins on diversity. It is a shame that this wasn't the final as both zoos have large and diverse collections.