The enemies within Darwinia are different forms of viruses.
| Name | Description |
|---|---|
| Virii | The basic enemy, appearing as red triangles within a line. Wanders randomly around a given location, but will try attacking anything that enters its range. |
| Bug | |
| Centipede | A stronger version of virii. WHen hit, it will break into individual centipedes, but will flee. |
| Spider | Attacks by leaping into targets. Immune to lasers. |
| Soul Destroyer | A powerful virus that kills targets. Normally, a destroyed Darwinian leaves a green soul, but this virus will consume these souls. |
| Spore Generator | A hovering enemy that lays eggs to create new viruses. |
| Triffid | Periodically fires an egg, which creates new virii or other enemies at a location. They will shell a given area at a distance once it detects an intruder. |
| Army Ant | Attacks anything in range of the nest, and also collects souls back to produce more ants. |
The quantity of enemies is affected by the difficulty setting within the options menu.