Arsenic (As) is known to disrupt the biological function in plants by inhibiting their growth and developmental process, while selenium (Se) is an essential micronutrient within the appropriate amount. Phytohormone auxin on the other hand is an established growth regulator and plays a significant role in stress management. Present study is designed to see the effect of Se and auxin on morphological and biochemical characteristics and, on the genotoxicity in rice plants under As stress. The observations indicated that seedlings supplemented only with As showed inhibition in the growth parameters, however, co-application of Se and auxin improved growth of rice seedlings, level of stress indicators, (chlorophyll, protein, MDA content) and modulators (cysteine, proline) as compared the individual treatment of As. Genomic template stability calculated through changes in RAPD profile showed consistent results when compared with the indicator and modulator parameters. Altered DNA profile showed varying degrees of polymorphism, highest in roots of As treated seedlings and lowest in roots of Se + auxin and As + Se treated seedlings. Altogether, this study conclude that application of Se and auxin alone or in combination were more effective in lowering the As induced stress in rice. (C) 2015 Elsevier B.V. All rights reserved.