Drought stress is one of the most important factors limiting maize production. Rab17 is an ABA-responsive gene and associated with drought tolerance. In order to identify haplotypic structure and mine allelic variants at rab17 locus, nucleotide diversity and linkage disequilibrium (LD) structure of rab17 were evaluated among a mini core set of Chinese diversified maize inbred lines. Totally, 19 SNP and 18 insertion/deletions (InDels) were identified, among which 81% were in non-coding regions and 19% in coding regions. The results showed that a high level of diversity appeared within 1 kb upstream of the rab17 locus, and declined quickly downstream of the gene region. Rapid decay of linkage disequilibrium of rab17 region with distance within 1 kb was detected. Functional markers which can be developed based on haplotype 14 are expected to have contribution to molecular breeding for drought tolerance. Drought stress is one of the most important factors limiting maize production. Rab17 is ABA-responsive gene and associated with drought tolerance. In order to identify haplotypic structure and mine allelic variants at rab17 locus, nucleotide diversity and linkage disequilibrium (LD) structure of rab17 were considered among a mini core set of Chinese diversified maize inbred lines. Totally, 19 SNP and 18 insertion / deletions (InDels) were identified, among which 81% were in non-coding regions and 19% in coding regions. The results showed that a high level of diversity within 1 kb upstream of the rab17 locus, and declined quickly downstream of the gene region. Rapid decay of linkage disequilibrium of rab17 region with distance within 1 kb was detected. Functional markers which can be developed based on haplotype 14 are expected to have contribution to molecular breeding for drought tolerance.