Coccinia grandis L (Family Cucurbitaceae), a perennial dioecious herb with heteromorphic sex chromosomes has the quality of a model plant for analysis of sexual evolution in angiosperms. Yet, little is known about the physical side, genetic orientation and substitution behavior of key gender-defining factors in this important plant species. Screening of genomic DNA with RAPD primers was used for sex diagnosis and gender specificity of C. grandis in this study. Bulk analyses of pooled DNA from male and female genotypes resulted in the isolation of a putative male specific sex marker CgMSM. A sequence characterized amplified region (SCAR) marker CgY1 designed from CgMSM amplified an 829 bp fragment in the male C. grandis but not in the female plants. Southern blotting confirmed it as a single copy locus in the male genome. Further, the CgY1 marker accurately identified 11 male and 6 female genotypes from 17 individuals of C. grandis with unknown sex. Sequence homology revealed high similarity between CgMSM (CgY1) and the putative MADS-box domain of the APETALA3 (AP3) MADS-box gene which is responsible for development of petals and stamens in flowering plants. Thus, the SCAR marker CgY1 could be used as an efficient tool for early sex identification in C. grandis and forms the basis for characterization of genes associated with evolutionary pathways in sexual dimorphism. (C) 2014 Elsevier B.V. All rights reserved.