Linkage or association of genetic markers to quantitative traits of agronomic importance can substantially simplify the genetic analysis of complex quantitative traits. Enzyme marker genes are ideal candidates for quantitative genetic analysis. We have recently applied this powerful methodology to the analysis of genetic resources of wild cereals in Israel, primarily wild emmer wheat, Triticum dicoccoides, and wild barley, Hordeum spontaneum, the progenitors of cultivated wheats and barley, respectively. We have found that allelic isozyme markers and ecological factors provide an important predictive method for identifying elite genotypes characterized by single or multiple disease resistances, high protein content, and a variety of quantitative traits of agronomic importance including germination, earliness, biomass, and yield variables. Our predictive methodology could be improved by additional crossing tests in an attempt to verify the results derived from the correlation analysis and thus establish the linkage relationships between the marker gene and the quantitative trait under discussion. This methodology, if further developed by additional isozyme and DNA markers, verified by crossing tests and gene mapping, could substantially contribute to the sampling and utilization of the genetic resources of wild gene pools for crop improvement.