The invention relates to a codominant SSR marker closely linked with a black shank resisting gene qBS01 of cigar Beinhart1000-1 and application thereof; the black shank resisting gene qBS01 is a quantitative character gene locus derived from the cigar variety Beinhart 1000-1 and has black shank No. 0 and No. 1 physiological race resistance. The codominant SSR marker closely linked with the cigar Beinhart1000-1 black shank resistant gene qBS01 has the serial numbers of TMc14137 and TMc14142, wherein the nucleotide sequences of PCR amplification products of the codominant SSR marker closely linked with the cigar Beinhart1000-1 black shank resistant gene qBS01 are respectively shown as SEQ ID No.1, SEQ ID No.2, SEQ ID No.3 and SEQ ID No.4. In addition, the application is the application of the codominant SSR marker closely linked with the black shank resistance gene qBS01 of the cigar Beinhart1000-1 in detecting whether the black shank resistance gene qBS01 exists in a tobacco genome DNA (Deoxyribose Nucleic Acid) or not. The codominant SSR marker disclosed by the invention has the characteristics of rapidness, stability, accuracy and low cost, so that the molecular marker can be applied to qBS01 gene molecular marker-assisted selection in disease-resistant breeding of No. 0 and No. 1 physiological races of tobacco black shank.