The "Unknown Root" is the concept of "that which was before all others." This is a generic expression that can be used in many religions and beliefs (usually of a gnostic or esoteric nature.) This concept of an "unknown root" is meant to represent the "One True God" or force that is above all else. The unknown root is the beginning of all things.
This term can be used interchangeably with a number of other terms and phrases that denote the same meaning of a "first god" concept.