Digital PCR (dPCR) is the third generation of PCR for the absolute quantification of nucleic acids in the reaction without a standard curve by partitioning reactions. In recent years, various dPCR platforms have been developed and used in a variety of research and diagnostic applications. dPCR technology has significant potential as a tool for detecting species identification markers in large samples through accurate quantification of absolute copy numbers. In this chapter, we describe the dPCR detection method for discovering molecular markers used for Hanwoo cattle breed identification using three types of digital PCR platforms (Bio-Rad, Stilla technologies, and OPTOLANE).