The invention relates to the field of biotechnology, in particular to an SNP marker as well as application and a detection method thereof. A great amount of individuals of Chinese Apis mellifera are subjected to whole genome sequencing, so that 21 specific SNP messages in the Chinese Apis mellifera are obtained and the 21 specific SNP messages serve as marker SNP sites for identifying the Chinese Apis mellifera. The special SNP sites in the Chinese Apis mellifera provided by the invention play an important role in the differentiation of the Chinese Apis mellifera with the Apis mellifera in other regions as well as in the adaptive evolution of the Chinese Apis mellifera to local environment.