Calamus guruba Buch.-Ham., a perennial, dioecious rattan species of the family Arecaceae has recently emerged as an important source of tribal economy owing to its high-quality flexible canes for furniture manufacturing and cottage industries. The dioecious nature together with disproportionate distribution of male and female sex organs has been the major constraint in the development of an effective breeding programme for the plant. Early identification of the male and female genotypes at the seedling stage is a pre-requisite to ensure genetic improvement of C. guruba. In the present study, we used 30 inter simple sequence repeat (ISSR) markers to develop a sequence-tagged site (STS) linked to male sex in C. guruba. Molecular analysis of bulked DNA pooled from male and female genotypes resulted in the isolation of a putative male-specific marker CgMSM. Partial sequencing of CgMSM resulted in an STS marker CgMY1 which could successfully amplify a 597-bp fragment in male but not in the female plants. DNA gel blot analysis confirmed it as a single-copy locus in the male genome of C. guruba. Further validation of CgMY1 in the natural population of C. guruba resulted in precise detection of 9 males and 6 females from 15 individuals with unknown sex. Therefore, the STS marker CgMY1 could be used as a proficient tool for early sex differentiation and form the basis of a sustainable breeding programme for genetic improvement of C. guruba.