In Animal Farm, how do the animals identify an enemy?

Anything that goes on two legs is an enemy.

When the animals expel the humans from Animal Farm, they follow Old Major’s advice about who their friends and who their enemies are. Old Major was very specific. He gave the animals a long litany of abuses perpetrated by humans and then proclaimed that humans were the enemy.

Because nearly the whole of the produce of our labour is stolen from us by human beings. There, comrades, is the answer to all our problems. It is summed up in a single word−Man. Man is the only real enemy we have. Remove Man from the scene, and the root cause of hunger and overwork is abolished for ever. (Ch. 1)

Since some of the animals are not that bright, Old Major seeks to solidify and simplify his pronouncement into one simple slogan that all animals can follow.

I merely repeat, remember always your duty of enmity towards Man and all his ways. Whatever goes upon two legs is an enemy. Whatever goes upon four legs, or has wings, is a friend. (Ch. 1)

The animals make this statement into their second commandment: Whatever goes upon four legs, or has wings, is a friend. Snowball then further reduces the idea into “the essential principle of animalism,” which is "Four legs good, two legs bad." Old Major says that the animals should never trade with people or imitate them.

The pigs do not go long before they break this rule. They slowly add more and more trappings of humanity. Before long, the pigs are wearing clothes, sleeping in beds, and walking on two legs. They finally replace all of the tenets of Animalism with one: “ALL ANIMALS ARE EQUAL BUT SOME ANIMALS ARE MORE EQUAL THAN OTHERS” (Ch. 9). This means that the pigs are superior to the other animals, and Old Major’s dream of equality is dead.