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Seed categories and crop varieties play an important role in wheat production in Egypt, which effect on genetic purity of wheat genotypes. So, this investigation aimed to study the effect of seed sources and varieties on yield and its attributes. Two field experiments were conducted at the Experimental Farm of Giza Agricultural Research Center (ARC), Giza Governorate, Egypt, during two successive winter growing seasons of 2014/2015 and 2015/2016 on the optimum sowing date 15th of November. Four wheat varieties (Misr1, Gemmeiza 11, Giza 168 and Sids 12) and their seed categories (Basic, Certified and Farmer saved seeds) were used in this study. Yield and its attributes and off- type percentage were estimated in the field experiment, further more phenol color reaction and ISSR technology were carried out at Seed Technology Department Laboratory. The results indicated significant differences between wheat varieties and its seed categories for the most traits. Gemmeiza 11 variety gave the highest value in most studied traits i.e., flag leaf chlorophyll content SPAD, flag leaf area, spike length, No of spikes/m², No of grains/spike, 1000-grain weight and grain yield/fad., while the lowest value of those traits were recorded by Misr 1 variety. For the effect of seed categories on yield and yield attributes, basic seeds gave the greatest value for all characters, except for plant height where farmer seed recorded the highest value. Meanwhile insignificant effects were obtained from seed categories on flag leaf chlorophyll content SPAD. The interaction effects between varieties and seed categories indicated that Gemmeiza 11 and Sids 12 varieties with Basic and Certified seed categories gave the highest value of most traits, while Misr 1 Varity with farmer seed category gave the lowest value for yield traits. Insignificant effects were noticed between wheat varieties for the off- type % while seed categories showed highly significant effects where, Farmer saved seed recorded the highest value and Basic seed gave the lowest value for this trait. Wheat varieties showed different color reaction to phenol while seed categories took the same pattern in phenol color reaction for each variety. Eight ISSR primers were used for fingerprinting the four wheat varieties and their seed categories produced 97 band, 31 of them were polymorphic (68.04%) polymorphism. The highest level of polymorphism was observed in primer HB-12 which showed 95.00% polymorphism, while the lowest polymorphism was 28.57% in primer HB-09. [ABSTRACT FROM AUTHOR]