Squirrels protect themselves by running, hiding and fighting. Fighting, such as scratching and biting, is usually a last-ditch effort for squirrels. Running and even camouflaging themselves are their first instincts when faced with possible danger.
According to Welcome Wildlife, squirrels run and even swim when evading pursuers. At other times, they remain perfectly motionless and camouflage themselves against the bark of trees. Squirrels also like to keep objects such as tree trunks between them and danger. Because trees are so important to their natural defenses, squirrels hunt and build nests in them.
Some species of squirrel are more aggressive than others. For instance, the red squirrels of Minnesota are more likely to fight off attackers if they must. This aggressive behavior extends to other squirrels even of the same species. They're fiercely territorial, and each squirrel has its own acre or two of space.
The California ground squirrel, on the other hand, developed specific protective techniques through evolution and adaptation. This species is immune to the venom of the Northern Pacific rattlesnake, its neighbor and natural predator. This species also signals with its tail, called a tail-flag, in order to warn off the snake and let the snake know that it knows the snake is there.