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Auxin is well known to stimulate coleoptile elongation and rapid seedling growth in the air. However, its role in regulating rice germination and seedling establishment under submergence is largely unknown. Previous studies revealed that excessive levels of indole‐3‐acetic acid(IAA) frequently cause the inhibition of plant growth and development. In this study, the high‐level accumulation of endogenous IAA is observed under dark submergence, stimulating rice coleoptile elongation but limiting the root and primary leaf growth during anaerobic germination (AG). We found that oxygen and light can reduce IAA levels, promote the seedling establishment and enhance rice AG tolerance. miRNA microarray profiling and RNA gel blot analysis results show that the expression of miR167 is negatively regulated by submergence; it subsequently modulates the accumulation of free IAA through the miR167‐ARF‐GH3 pathway. The OsGH3‐8 encodes an IAA‐amido synthetase that functions to prevent free IAA accumulation. Reduced miR167 levels or overexpressing OsGH3‐8 increase auxin metabolism, reduce endogenous levels of free IAA and enhance rice AG tolerance. Our studies reveal that poor seed germination and seedling growth inhibition resulting from excessive IAA accumulation would cause intolerance to submergence in rice, suggesting that a certain threshold level of auxin is essential for rice AG tolerance. Summary statement: Excessive auxin accumulation negatively affects rice AG. Conversely, oxygen and light significantly reduce IAA levels, promote the seedling establishment during AG, and submergence‐repressed miR167 reduces IAA levels through miR167‐ARF‐GH3 pathway and enhances AG tolerance. [ABSTRACT FROM AUTHOR]