Fahima's research interests have focused on the application of plant genomics for characterization, utilization and conservation of wild cereal populations in Israel (mainly wild emmer wheat, Triticum dicoccoides, and wild barley, Hordeum spontaneum). His laboratory is involved in plant structural and functional genomics studies, and population genetics of wild cereals. The genomic studies include molecular marker development, linkage mapping, quantitative trait locus (QTL) analysis, map-based cloning, and maker-assisted selection of several traits with economic values, such as disease resistance, grain protein and mineral content, and drought resistance. Fahima's lab was involved in the positional cloning of the high grain protein QTL, Gpc-B1, and the high-temperature stripe rust resistance gene, Yr36, both derived from wild emmer wheat. Tzion Fahima is a Corresponding member of the European Cooperative Program for Crop Genetic Resources (ECPGR) Network organized by the International Plant Genetic Resources Institute (IPGRI) of the European Community, a member of the Scientific Board of the Israeli Gene Bank (IGB) for Agriculture Crops, a member of the Coordination Committee of the European Triticeae Genomics Initiative (ETGI), and a member of the International Wheat Genome Sequencing Consortium.