Abstract: A humidity control system employed on a container refrigeration unit, and method of controlling the container humidity, that includes a computer controller and utilizes a humidity sensor, a moisture supply system in combination with output drivers to control and limit the level of relative humidity level within a cargo container to a predetermined range when normal refrigeration system controls are active. The humidity control system operates the moisture supply system in a manner that significantly maintains a high, but not excessive, level of moisture in the circulating air and in the stored cargo. The humidity control system can also be configured to operate as a stand-alone system thereby eliminating the need to provide additional evaporator fan controls for the refrigeration unit.