To explore the molecular basis for an individual with CisAB subtype of the ABO blood group.ABO antigen and serum antibody of the proband were detected with a serological method. Exons 5 to 7 of the ABO gene were amplified with PCR and sequenced bidirectionally. Allele-specific amplification for exon 6 to 7 was also carried out.The proband was assigned as a CisAB phenotype based on his serological characteristics. Heterozygous variations including 220C/T, 261G/del, 297A/G, 467C/T, 646A/T, 681A/G, 771C/T, 803G/C, 829A/G and 1009A/G of the ABO gene were identified through direct sequencing, which was assigned as CisAB01var/O02 genotype. Allele-specific amplification indicated that the proband carried an O02 allele and a CisAB01var allele. Compared with A102, the CisAB01var allele has two nucleotide substitutions at 803G>C and 1009A>G, which resulted in replacement of amino acid Gly by Ala at position 268 and Arg by Gly at position 337.The CisAB subtype was identified with 803G>C and 1009A>G variants in the α1,3-N-acetyl-galactosaminyltransferase gene compared with that of the A102 allele.