The invention discloses a primer group for identifying cotton seeds and a kit thereof. The primer group comprises 60 pairs of core primers, and the core primer group disclosed by the invention provides a powerful tool for identifying cotton varieties in production, has the advantages of quickness, accuracy and the like, provides a powerful identifying tool against fake and forged commodities, fake plate and fake commodities and other events cheating and harming farmers, which occur during the future production, provides a reliable method and technical guarantee for handling problem seeds by a local seed management department, and greatly protects cotton breeders, seed production and operation units and production benefits of the majority of cotton farmers. The set of core markers are used for identifying fingerprints of the varieties and the screening of a large number of molecular markers is not required, thus the cost and the time are saved, and the effect of achieving maximum results with little effort is achieved.