Pointed gourd (Trichosanthes dioica Roxb.), a perennial dioecious plant of the family Cucurbitaceae has recently emerged as an important cash crop due to its great medicinal and nutritive value. Breeding programmes in pointed gourd have several constraints such as poor germination, vegetative means of propagation and dioecy. Identification of male and female at the seedling stage is a pre-requisite for the genetic improvement of this species. Screening of genomic DNA with inter simple sequence repeat (ISSR) primers was used for early detection of male and female plants in this study. Using pooled DNA from male and female genotypes and 40 ISSR primers, a putative male specific marker TdMSM was produced. It was converted into a sequence tagged marker TdSTSM which could successfully amplify 720 bp product in male but not in the female. Southern blotting confirmed it as a single copy locus found only in male plant. Further, the TdSTSM marker was used to accurately detect 9 males and 6 females from 15 individuals of pointed gourd with unknown sex. Thus, the STS primers designed from ISSR fragment TdMSM could be used as an effective and reliable molecular marker for early sex diagnosis in T. dioeca. (C) 2012 Elsevier B.V. All rights reserved.