Plant molecular identity (ID) is used to describe molecular characteristics of plants, which should contain all of the necessary information. Using inter-simple sequence repeat (ISSR) primers, molecular ID can be described in a way that reflects the polymerase chain reaction (PCR) conditions, annealing temperature, and the bands obtained in PCR amplification. A new complete molecular ID system is described in this study, which can be easily used and expanded to include more information. Using three cotton cultivars, we analyzed the products of PCR with ISSR primers and discussed the strategy for establishing their molecular ID. Using the segmented naming method, we designate the simple names and the full name systems of these three cultivars.