Genetic diversity at 28 microsatellite loci was studied in a natural population of Triticum dicoccoides at the Ammiad microsite, north of the Sea of Galilee, Israel. This microsite was subdivided into four major habitats, North, Valley, Ridge and Karst, and further subdivided into nine subhabitats. The units thus defined showed strong and highly significant differentiation in ecological factors; in particular with respect to cover, proximity and height of rocks, and surface soil moisture after early rains. The results showed that allele distributions at microsatellite loci were nonrandom and associated with habitats. Significant genetic differentiation and variation in repeat number were found among subpopulations in the four major habitats and nine subhabitats. Habitat-specific and -unique alleles and linkage disequilibria were observed in the Karst subpopulation. The subpopulations dwelling in drier habitats and subhabitats showed higher genetic diversities at microsatellite loci. These results suggest that natural selection, presumably through aridity stress, acts upon microsatellite divergence predominantly on noncoding sequences, thereby contributing to differences in fitness.