Drought stress is a major constraint in many maize production areas of the world. Association mapping is an alternative method for mapping candidate genes and QTLs responsible for phenotypic variation in important agronomical traits. This research was conducted to i) test statistical associations between RFLP marker alleles and phenotypic variation for anthesis-silking interval (ASI) and grain yield (GY) traits recorded under drought stress and well-irrigated conditions, and ii) asses the linkage disequilibrium for each pair of loci for the line set. Thirty tropical maize inbred lines were planted in two side-by-side field experiments (well-watered and drought stress conditions), at two locations in Mexico, during the dry-season 2003, and one-greenhouse experiment at the University of Nebraska-Lincoln. The set of lines can be classified into 15-drought selected, one drought susceptible and 14-drought unselected lines. Those lines were evaluated in a 5 x 6 rectangular lattice design with three replications. DNA of each the 30 lines was digested separately with EcoRI and HindIII and Southern blots were hybridized with 62 RFLP probes. Significant differences among inbreds for ASI and GY were found in all the experiments suggesting the presence of a broad genetic variation for these traits among the set of lines.Twenty five percent of the loci showed significant association with ASI. Six RFLP probes were consistently associated with ASI as observed from the polymorphism in both enzymes. Strong association was found between markers of bnl6.29 and umc66 (in both enzymes) and variation in ASI among lines. QTLs for this trait have been previously reported in the chromosomal regions where this probes map (chromosome 2 and 8, respectively). On the other hand, six loci showed significant association with ASI, which allowed certain degree of separation between tolerant and conventional lines. Nine percent of the loci pairs showed significant LD (at P < 0.01).