Brassicaceae family (Cruciferae) known as mustard family, it is one of the largest families of flowering plants which have 372 genera and 4060 species all around the world. This study aims to investigate comparatively  the anatomical structure  of  some plant samples of this family. Anatomical sections were taken on both stems and leaves, and 42 different qualitative characters were recorded in a data matrix. The results were numerically analysis to know the similarity between these samples by draw a dendrogram.  Then the anatomical results were used to determine the genetics relationships between studied cultivated genera and the wild genera in order to includ in the breeding and improvement programs. Scot methods was chosen as it is fast, effective and gives accurate results. Start codon targeted (SCoT) polymorphism are one of the common markers were used to assess genetic diversity in some genera in Brassicaceae family. Seventin genera of the Brassicaceae have been used with ten SCoT primers. Totally, 174 bands were scored out of which 84.5% showed polymorphism, where 149 polymorphic bands and 25 monomorphic bands were observed. The results indicated that the existence of a significant degree of genetic similarity ranged from 0.62 to 0.88, where the highest mean value was 0.88 between genera 12 (Morettia canscens) and 13 (Moricandia siniaca) and the lowest mean value was 0.62 between genera 2 (Brassica napus) and 15 (Sinapis alba).