The esterase (EST) and the malate dehydrogenase Ⅱ (MDHⅡ) isozymes in A. mellifera carpatica (C), A. mellifera ssp.(D), “Zhejiang Agricultural University No.1” A. mellifera ligustica (Ea) and A. mellifera carnica (K), and the genotypes of MDHⅡ isozymes in four subspecies of A. mellifera were analysed by IEF PAGE. The results indicate that the four subspecies of A. mellifera showed the same EST zymogram, while A. cerana showed a different EST zymogram, which suggests that the genotypes of EST isozymes in A. mellifera are different from those in A. cerana. The genotypes of the MDHⅡ isozymes in four subspecies of A. mellifera were aa, ab, ac, bb, bc and cc. The C and Ea subspecies exhibited high homozyosity, while D and K displayed high heterozyosity. The allele b appeared to be the highest frequency in C, while the allele c had the highest frequency in Ea. The frequencies of the alleles a, b and c in sub species D were very similar. The alleles a and c were common, while allele b was rare in sub species K. There were highly significant differences in genotype frequencies, allele frequencies, homozyosity and heterozyosity among these four subspecies.