The present study was carried out for the comparison of RAPD and ISSR markers for polymorphism pa ern and molecular diversity analysis among 17 ridge gourd (Luff a acutangula L.) and sponge gourd (Luff a cylindrica L.) genotypes using 20 RAPD and 12 ISSR markers. Twenty RAPD primers generated total of 94 bands of which 81 bands were polymorphic showing 86.17% polymorphism. The average bands per primer were found 4.05. The polymorphic information content (PIC) was recorded from 0.4828 to 0.8842 for RAPD. Jaccard’s similarity coeffi cient ranged from 30.8% to 78.6% for RAPD. However, out of 30 ISSR primers screened, twelve ISSR primers produced 79 bands of which 66 bands were polymorphic and 83.54% polymorphism with an average of 7.16 bands per primer. The PIC ranged between 0.6548 and 0.8939 for ISSR. Jaccard’s similarity coeffi cient ranged from 22.7 % to 81.2% for ISSR. This study showed that RAPD and ISSR markers produced specifi c DNA fragments for identifi cation of ridge gourd and sponge gourd genotypes.