In Date palm (Phoenix dactyliferaL.) molecular characterization to find the best genotype and male/female identification at an early stage before flowering is of great economic significance for farmers. Genetic finger printing using molecular markers is an important tool. In present investigation two types of marker viz., RAPD and ISSR were applied in 8 Date palm genotypes and five types of markers RAPD, ISSR, SSR, ITS and 18s rRNA gene were applied in 5 genotypes of Date palm (Ghanshyam, Early maturing, Late maturing, Male 2 small and Male1 tall) and at the same time Ghanshyam was also screened with its 14 seedling genotypesRAPD markers were more efficient than ISSR assay with regard to polymorphic detection; RAPD markers detected 36.84% polymorphism as compared to 0.12% by ISSR markers. Cluster analysis by UPGMA shows that the dendrogram obtained was similar for RAPD and RAPD + ISSR, In other case study of 5 Date palm genotypes (Ghanshyam, Early maturing, Late maturing, Male 2 small and Male1 tall), five type of markers with one best primer for each marker (RAPD, ISSR, SSR, ITS and18s rRNA) were used.