Seaweeds are commercially important crops and hence their taxonomic identification plays a significant role. Due to high species diversity, the delineation of species of the family Gracilariaceae has always remained difficult. Phenotypic plasticity among the species of Gracilaria is the cause for the difficulty in identifying its species. Hence, molecular analyses in combination with morphological studies are crucial for better identification of Gracilaria species. Five morphological variants of Gracilaria corticata were collected from different locations of East coast of Tamil Nadu, India. Random Amplified Polymorphic DNA analysis (RAPD) was used to investigate molecular characteristics of the five variants. ISSR markers were also used to determine the genetic variation and results of this study revealed that ISSR markers could be used efficiently for genetic differentiation of G. corticata individuals of different regions. Intraspecific variation among the variants of Gracilaria corticata was studied with mitochondrial Cox1 as DNA barcoding marker gene. Based on the sequence result accession numbers were obtained for the variants viz., Gc1(MN781148), Gc3(MN813485), Gc4(MN813486) and Gc5(MN813487).