In the past, the genetic diversity in jute has been studied but mainly using morphophysiological traits. This method is slow and unreliable, and phenotypic identification based on morphological traits is subject to environmental variation (Palit et al., 1996; Cooke, 1999). This limitation can be overcome by the use of molecular markers that are not influenced by the environment and are useful for the evaluation of genetic diversity, germplasm collections and markerassisted breeding (Mir et al., 2008; Banerjee et al., 2012).