The present invention includes a system for marking labware. The system includes an instruction set with markings to be applied to pieces of labware and the order in which the markings are to be applied to the labware. The system also includes a marking device that receives the instruction set and then places the non-toxic marks on the pieces of labware. The invention also includes methods tracking chain of custody of biological material in a facility. The methods include assigning a unique marking for biological materials, storing that marking in a database, applying a non-toxic marking to a piece(s) of labware and then scanning the marking.