Twelve mango cultivars grown in the Egypt were discriminated by their seed SDS-protein and PCR- based molecular markers. For PCR analysis three different techniquess were used including novel technique. Comparitive analysis were conductied beween the two old technique, ISSR and RAPD, and the novel tecnique, three primers-based RAPD. The cultivar- specific markers represented 24.46%of the total markers (regardless of type of analysis), 88.89% of them were RAPD markers. Most of these markers were scored for the presence of unique bands. Cultivar- specific markers were shown to be useful in constructing linkage map that involve any polymorphic gene(s). Dendrogram tree generated across SDS-protein, RAPD, ISSR and three promers- based analysis. Constructed dendrograms for results, individually or collectively, revealed that similarity and clustering is dependant on the marker system used.