This study investigated the effects of retrotransposon movements on the regeneration of 15- and 30-day-old leaves and roots of four different rice varieties grown in tissue culture medium at different salt concentrations (0, 50, 100, and 200 mmol/L) by Inter Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) polymerase chain reaction (PCR)-based marker methods. The study used Hopi, Houba, Osr30, Tos17 primers for IRAP analysis. The (GA)9C ISSR primer was used with four IRAP primers in REMAP analyses. There were different band profiles and polymorphism results between different salts concentrations of the same variety and various rice varieties. We observed that the polymorphism ratios for Houba ranged from 0 to 98% in IRAP and REMAP analyzes in the calculation made with the Jaccard similarity index in mutant samples. We report that mutant varieties give more valuable IRAP and REMAP results than non-mutant varieties. The results reported in this study contribute to understanding the effect of salinity stress on rice in terms of retrotransposon-based molecular markers. These results suggest that all tested retrotransposons are still active, causing genomic polymorphism among rice plantlets.