Apparatus for a cotton sample acquisition and tracking system. The system includes a loading station in which a pair of primary sample halves are loaded in a carrier. The primary samples are identified and transported to a sub-sample station that extracts a sub-sample from the primary sample. The sub-samples are conditioned and transported to various testing stations. The primary samples are transported via a conveyor system. The sub-samples are transported through a pneumatic system. The sub-sample station advances the primary sample against a pick drum that pulls tufts from the primary sample. The tufts flow through a cotton containment system into an indexer that collects, conditions, and routes the tufts as a sub-sample. The sub-samples are staged in a carousel for continued conditioning and storage until the test equipment is ready to process the sub-sample.