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Cardiospermum halicacabum is one of the most important medicinal plants of sapindaceae. The present work initiate comparative pharmacognostic study on Cardiospermum halicacabum L. var. microcarpum (Kunth) Blume and var. luridum (Blume) Adelb, through macroscopic and microscopic characters of seeds. Both the varieties of C. halicacabum are called by one vernacular name ‘Mudakkatran’. These two varieties have distinctive features both in morphology and anatomy. The two varieties of C. halicacabum are used medicinally one for the other. Most of the characters are similar but the variations occur in the leaves and seeds. The results of the present study showed diagnostic character and differences among the two varieties. Hence, plant anatomy is one of the alternative steps to differentiate the plant species.