In this paper I challenge the claim that Bacon considered the operation of species as limited to the physical and sensory levels and demonstrate that in his view, the very same species issued by physical objects operate within the intellect as well. I argue that in Bacon the concept of illumination plays a secondary role in the acquisition of knowledge, and that he regarded innate knowledge as dispositional and confused. What was left as the main channel through which knowledge is gained were species received through the senses. I argue that according to Bacon these species, representing their agents in essence, definition and operation, arrive in the intellect without undergoing a complete abstraction from matter and while still retaining the character of agents acting naturally. In this way Bacon sets the intellect as separate from the natural world not in any essential way, but rather as it were in degree, thus supplying a theoretical justification for the ability to access and know nature.