Indigofera cordifolia Heyne ex Roth. so far is reported only in the Arabian Peninsula from Oman. A recent field expedition in the Farasan Archipelago, Saudi Arabia, Red Sea, resulted in documentation of this species in Dumsuk Island. Morphological examination and molecular identification based on the nuclear ribosomal DNA internal transcribed spacer region of this plant species was investigated in this study. The result show that the internal transcribed spacer had high species-level discrimination efficiency for the identification of Indigofera cordifolia that may provide help in authentic identification and management process of this rare and nationally endangered species.