A DNA marker linked to the columnar gene (Co) in apple (Malus domestica) was explored based on the population of 105 progenies of 'Spur Fuji' x 'Telamon' by bulk segregant analysis (BSA) and Random Amplified Polymorphic DNA (RAPD) technique. A total of 300 random primers were screened and a RAPD marker (S1142(682)) closely linked to Co gene (2.86 cM) was identified and then sequenced. Four specific PCR primers (two forward primers and two reverse primers) were designed,and the products of SCAR-PCR indicated that all the four pairs of primers could amplify polymorphic bands between columnar and non-columnar traits, so any of them could serve as the specific SCAR primers. One pair of these specific primers was chosen to amplify each individual in the population, and the result showed that the co-segregation pattern of this SCAR marker and Co gene was the same as that of the RAPD marker. Furthermore, it was found that the nucleotide sequence of the RAPD marker fragment contained an open reading frame (ORF) that could encode 68 deduced amino acid residues at the position of +45 - +251.