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Pergularia daemia. and Verbesina encelioides are commonly occurring annual medicinal plants in arid and semi arid regions of India, however, identified as weeds of cultivated and fallow lands. Polymerase chain reaction technique has seen standardized for the detection of phytoplasmas causing witches’ broom, phyllody in Pergularia daemia (Forsk.) Chiov. and Verbesina encelioides (Cav.) Benth. & Hook using two sets of forward and reverse primers of 16S rRNA spacer region and 16S of rRNA were specifically amplified by PCR. The results indicate that PCR based diagnosis can be used for the detection of phytoplasmas in P. daemia (Forsk.) and V. encelioides. Samples of both infected plant species proved positive for the presence of Phytoplasma. PCR amplification of 16S rDNA technology has significantly;contributed to the identification and characterization of unidentified Phytoplasmas. A band of approximately 1.2 kb was consistently observed to be amplified from total DNA extracted from infected samples. The association of Phytoplasma with witches’ broom and phyllody diseases of P. daemia and V encelioides was confirmed by PCR-amplification.