Wheat (Triticum aestivum L.) is a major crop for human consumption and consider one of the world's major cereal crops. The present study conducted at the Farm and Labs of the Faculty of Agriculture, Saba Basha, Alexandria University, Egypt to study the different morphological, biochemical and molecular characteristics between some Egyptian and Libyan wheat cultivars during 2015/2016 and 2016/2017 seasons to estimate the genetic relationship. Based on morphological data the general genetic similirity between all wheat cultivars was 76%, the culster divided into two main groups e.g. the first group includes four Libyan wheat cultivars and the next group from the main culster includes all the Egyptian wheat with one cltivar from Libya (Sohag), The same results were found to Gemmeiza 9 was the onlyest cultivar in one custer by shareing the other Egyptian wheat. In total of 8 enzyme loci, three anodal and five cathodal loci were detected. One anodal (Pex.2a) was found as common band for all the cultivars for the positive charge. While three cathodal (pex 1c, pex 1c and pex 1c) were found to the negative charge. Pex.1a was found as unique for Egyptian wheat and (pex c4) was unique for Libyan and Egyptian wheat cultivars i.e. Sohag, Kofra, Kazeno, Kerem, Shakha 93 and Gemmeiza 9.Pex.5 was found in all wheat cultivars except Shakha 94. For the RAPD markers a total of 75 bands were detected among the studied cultivars. 53 bands showed polymorphism by 70.66 % genetic polymorphism. Out of these polymorphic bands, 13 unique bands were scored and the number of monomorphic bands was 9. These results could be helpful in study the genetic relationship between Egyptian and Libyan wheat cultivars.