Aromatic grass species Cymbopogon citratus (‘serai biasa/serai makan’) and C. nardus (‘serai wangi’) can be commonly found throughout Peninsular Malaysia. C. citratus is used in traditional Malaysian cooking and brewed as tea, while C. nardus is used in traditional medicine for external application and in insect repellents. Due to similar morphologies, it can be difficult to tell apart the species at times. Based on DNA sequence alignments of three chloroplast DNA intergenic spacer regions, namely atpB-rbcL, trnH-psbA and trnL-trnF, we designed species-specific primers for multiplex PCR assays for rapid species discrimination between C. citratus and C. nardus. The method described here makes use of simple molecular techniques that are time- and cost-effective for large-scale application. Such an assay will be useful for the quality assurance of food and medicinal products.