The present study was conducted in a private orchard during 2007 and 2008 seasons in order to evaluate the morphological, physiological characteristics and molecular marker in the two Indian jujube varieties, Balahy and Tofahy. The results showed that: Tofahy variety recorded the higher vigorous growth, leaf area, leaf length, leaf width and length of primary and secondary shoots, while Balahy variety recorded the higher leaf length/width ratio. Tofahy variety recorded the higher fruit set, fruit number/tree, fruit weight, yield, fruit width, fruit pulp thickness while Balahy variety recorded the higher fruit length, fruit length/width ratio, fruit firmness, seed weight and seed/fruit weight ratio. Tofahy variety recorded the higher fruit acidity, ascorbic acid while Balahy variety recorded the higher leaf and fruit total chlorophyll, fruit TSS/acidity ratio. Tofahy variety recorded the higher leaf and fruit nitrogen, phosphorus, calcium, magnesium, iron, manganese and zinc, leaf potassium and fruit sodium while, Balahy variety recorded the higher fruit potassium. No significant differences were recorded between both varieties concerning fruit drop, volume, TSS, reducing, non-reducing and total sugars, juice pH, chlorophyll A, B, carotene and leaf sodium. Genetic similarity was found for the two varieties in elecrophoresis analysis, but there were, little differences at the sequence of amino acids in protein and DNA bands.