Phenotypic identification of groupers of the genus Epinephelus is based on color patterns and a suite of morphologic characters. However, these characters often show intraspecific variations and differences between juveniles and adults of the same species. The present work is an attempt to study and ratify the status of Epinephelus spp. using random amplified polymorphic DNA (RAPD) analysis based on samples drawn from southeast and southwest coasts of India. The RAPD fingerprints generated in Epinephelus diacanthus, E. areolatus, E. chlorostigma, E. bleekeri, E. coioides, E. tauvina, and E. malabaricus with 4 primers (OPA 01, OPA 07, OPF 08, and OPF 10) were consistent, reproducible, and yielded species-specific diagnostic markers in all the species. A total of 59 RAPD loci in the size range of 70 to 4500 bp were produced from all 4 arbitrary primers. An unweighted pair-group method with arithmetic mean (UPGMA) dendogram was constructed based on genetic distance values to show the genetic relationships among the 7 species. All the individuals of each species formed monophyletic species clusters. The mean intraspecies genetic distance value (0.305) was significantly lower than the interspecies value (0.365). Epinephelus malabaricus was most distantly related to E. diacanthus and E. bleekeri. The genetic relationship was very close among E. coioides, E. tauvina, and E. malabaricus and also between E. chlorostigma and E. bleekeri. Within-species genetic polymorphism was highest in E. chlorostigma (49.15%) and lowest in E. tauvina (25.42%).