The purpose of this study was to investigate the role of silicon (Si)–mediated PIN gene expression and genotoxicity during arsenic (As) stress in rice. The objective was to examine Si-mediated differential expression of OsPIN genes, and their role in rice root architecture and genotoxicity based on the RAPD profile. The effects of Si on As-exposed rice seedlings of 7/15 days were analyzed. Root-related parameters (root volume, root length ratio, root mass ratio, root fineness, and root tissue density) were measured, followed by estimation and visualization of intracellular reactive oxygen species (ROS). Later, the impact of Si on OsPIN gene expression and changes in the random amplification of polymorphic DNA (RAPD) profile during As stress were accessed. Our results revealed that during As + Si treatment, higher expression of all 12 OsPIN genes was observed over As treatment. Furthermore, only OsPIN5c and OsPIN10b were induced in the presence of As relative to control; however, expression level was not influenced by the root morphology. Noticeable changes in root morphology and the RAPD profile, genomic template stability [GTS (%) = 62.50 and 79.36 in shoots, and 60.31 and 40 in roots of 7- and 15-day-old rice seedlings, respectively], and polymorphism (%) (37 and 34 in shoots, 40 and 38 in roots of 7- and 15-day-old rice seedlings, respectively) were observed upon the addition of Si with As. Overall, Si improved the root morphology by regulating the expression of OsPIN genes, ROS levels, and DNA stability.