Assessment of genetic diversity of crops by using informative molecular markers is important for their genetic improvement and conservation. Genetic diversity and relationships among seven Egyptian cultivars of wheat (Triticum aestivum L) (Masr1, Swiss2, Swiss4, Giza7, Giza9, Giza10 and Sakha94)were analyzed using SCoT and ISSR markers. A total of 7 SCoT and 7 ISSR primers were used to estimate genetic polymorphism among seven wheat cultivars (Masr1, Swiss2, Swiss4, Giza7, Gisa9, Giza10 and Sakha94) . DNA extraction was done using Thermo Kit according to its manufacturer's instructions followed by amplifications with ISSR and SCoT and agarose gel electrophoresis. Based on UPGMA both ISSR and SCoT markers resolved cultivars into dendrogram with three major clusters .The reproducible bands were scored for analyses polymorphic information content (PIC), Resolving power (RP) and Marker index(MI). Comparatively, two markers were effective. The average polymorphic information content (PIC), Resolving power (RP)and Marker index (MI) of SCoT were reflected relatively higher than those of ISSR. According to the present results, SCoT markers proved more informative in studying genetic diversity among seven wheat cultivars. The results demonstrated that SCoT and ISSR markers are useful for genetic diversity analysis of wheat cultivars. This information is useful for utilization in plant breeding programs.