India is the largest producer and exporter of turmeric (Curcuma longa), and different cultivars of this crop are traditionally characterized using agronomic traits, such as rhizome weight, yield potential, color and aroma of rhizome, curcumin content, and stability of curcumin content, which are influenced by environmental factors. The purpose of the present study was to probe whether karyomorphological and molecular marker attributes of turmeric cultivars could be correlated to validate their distinctiveness. Detailed karyomorphological analyses revealed uniform somatic chromosome number (2n = 63), with symmetric karyotype in all the studied cultivars. Chromosomes varied from 0.67 to 2.03 µm in length, with up to 72% bearing primary constrictions in the nearly median region (i-value ranging from 27.17 to 50). Asymmetry indices also indicated overall karyotypic symmetry among cultivars. On the contrary, random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) marker analyses revealed significant variability in the genetic constitution among them; Jaccard’s similarity coefficient value ranged from 0.569 to 0.969. Unweighted pair group method with arithmetic average (UPGMA) dendrogram and principal coordinate analysis based on the Jaccard’s coefficient produced four distinct clusters, which showed no geographical bias. Thus, it was concluded that although significant genetic variability that exists among the turmeric cultivars can be utilized for examining their authenticity, practicality of the use of karyomorphological characters for identification is significantly limited by the gross karyotypic similarity. Cryptic genetic changes accumulate in the genome of these plants because of their interaction with the environment. However, these remain confined within each cultivar in the absence of large-scale hybridizations and predominant vegetative propagation. This probably leads to variability in agronomic characters and may even help in developing novel characters in different cultivars. However, detection of any such change in the chromosomal structure would require fluorescent hybridization techniques. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.