Saracandra glabra (SG) is an important pharmaceutical plant with significant metabolically active bio-ingredients. Its extract contains powerful anti-inflammatory compounds which have a significant chemical, rheological, and pharmaceutical importance. The plant improvement programs need a rich resource of molecular markers. The lack of such markers for SG is a hindrance in molecular breeding for genetic improvement. The present work was done to enrich the molecular markers resource by identifying SSR, SNP and InDel markers from transcriptome data. Sarcandra glabra (Thunb.) Nakai and its subspecies S. glabra ssp. brachystachys were used to perform the transcriptome analysis.