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Cobitis bilineata is a species of ray-finned fish in the family Cobitidae found in Croatia, Italy, Slovenia, and Switzerland. Its natural habitats are intermittent rivers and freshwater marshes. It is not considered threatened by the IUCN.

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The Dalmatian barbelgudgeon is a European ray-finned fish species in the family Cyprinidae. It is the only member of the monotypic genus Aulopyge. The genus name is derived from the ancient Greek aulós + pygé, and thus means approximately "fluted tail-stem". The specific name honours the Austrian naturalist and diplomat Charles von Hügel. Though the genus was established in 1841, the species was only mentioned but not described at that time; that happened the following year, and in 1843, the frequently-seen misspelling huegeli was introduced. Many fish databases use 1843 as the year of description. The IUCN Red List uses 1842 and also has an explanation of the confusion here.

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Delminichthys adspersus is a species of cyprinid fish.

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The minnow-nase, Serbo-Croatian: podbila, is a species of freshwater fish in the family Cyprinidae. It is found in Bosnia and Herzegovina and Croatia. Its natural habitats are rivers, intermittent rivers, and inland karsts. It is threatened by habitat loss and considered Endangered (EN).

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The Neretvan nase or Dalmatian nase, Serbo-Croatian: podustva, is a species of freshwater fish in the family Cyprinidae. It is found in Bosnia and Herzegovina and Croatia.

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Ohrid trout or the Lake Ohrid brown trout is an endemic species of trout in Lake Ohrid and in its tributaries and outlet, the Black Drin river, in North Macedonia and Albania. Locally, the fish is known as охридска пастрмка in Macedonian and koran in Albanian.

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Phoxinellus alepidotus is a species of ray-finned fish in the family Cyprinidae. It is found in Bosnia and Herzegovina and Croatia. Its natural habitats are rivers and inland karsts. It is threatened by habitat loss.

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Squalius illyricus, the Illyrian chub, is a species of ray-finned fish in the family Cyprinidae. It inhabits karstic waters of Bosnia and Herzegovina, Croatia and Albania. Its natural habitats are rivers and water storage areas. It is threatened by habitat loss.

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Squalius svallize is a species of freshwater fish in the family Cyprinidae. It is found in Bosnia and Herzegovina and Croatia. Its natural habitats are rivers and inland karsts. It is threatened by habitat loss.

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Telestes turskyi is a species of cyprinid restricted to lake Buško Blato in Bosnia and Herzegovina and Čikola River, a tributary of the Krka in Croatia. This species was thought to be extinct, but was found in May 2002 by J. Freyhof and N. Bogutskaya. Its habitat continues to decline due to water extraction and drought.