Among the "invasive alien species" that countries must now eradicate or contain are grey squirrels, water hyacinths, and raccoons.
Other animals on the list include the Muntjac deer, which are in the UK, and the South American coati, which has been spotted in Mallorca, Spain.
Five species of crayfish are also on the list, along with three types of squirrel and the sacred ibis bird.
Each member state can decide how to tackle the blacklist.
Pets and zoo animals on the banned list can be kept until they die, while wild animals will likely need to be culled.
The EU describes an alien species as any organism that has been transported across ecological barriers like mountain ranges or oceans, becoming established in a new area.
It said that while many were brought to Europe intentionally "for their beauty, usefulness or commercial value", others have arrived by accident.
There are currently more than 12,000 alien species in the European environment, but the ones the EU is targeting are those which are invasive - "lacking predators or competition" to keep them in check.
Roughly 10-15% of alien species arriving in Europe eventually become invasive, according to the EU.
Some academics are concerned that the list is too short - it doesn't cover the notorious Japanese knotweed or common ragweed, for example.
Sven Bacher from Fribourg University in Switzerland told the New Scientist: "We are all a bit concerned with the low numbers of species on the list.
"We estimate there are around 1,000 to 1,500 invasive alien species in Europe and this is only a very poor selection."
The EU says the list is likely to be expanded in the future.
Flaviu the big cat spent three weeks out in the open after escaping from a zoo and was caught in a trap set by an expert.
Drones using thermal imaging cameras were used in the hunt for the animal after it disappeared shortly after arriving at Dartmoor Zoo in Sparkwell, near Plymouth.
The public had been warned not to approach the big cat and a large operation had been under way to track it down.
The alert went out on 7 July after keepers at the zoo found that the lynx, called Flaviu, had chewed through a board on the wall of his house and escaped.
The two-year-old Carpathian lynx had only recently arrived from Port Lympne in Kent.
The zoo owner, Benjamin Mee, told Sky News: "He weighed 20kg when caught, exactly the same weight as when he escaped."
Dozens of staff searched the zoo's boundaries and local nursery children were warned to stay indoors as the search continued with a police helicopter, but no trace of the animal was found.
The lynx, which is about the size of a labrador, was eventually caught with the help of an expert local trapper.
Mr Mee said: "Lynx willl always return to a kill. He hadn't made a kill, other than a rabbit which he ate. On Thursday evening he tackled a lamb which meant we knew he would be coming back to that site.
"When Flavio came back to finish his dinner he saw a big humane trap with meat in it. He was hungry, decided to take a chance, he went in. and we had him."
Carpathian lynx, which come from the mountain range in eastern Europe but are closely related to the much more widely distributed Eurasian lynx, normally feed on animals such as deer, hares, rabbits, rodents and grouse.
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