The invention discloses a ThRap2.1 gene for influencing submergence and waterlogging resistance of taxodium hybrid and application of the ThRap2.1 gene. The nucleotide sequence of the ThRap2.1 gene is shown in SEQID NO.1. According to the ThRap2.1 gene and the application thereof, the ThRap2.1 gene is transferred to woody mode plant poplars, the transgenic poplars with ThRap2.1 are overexpressed, the growth rate is reduced, internodes are obviously shortened, the expression quantity of ThRap2.1 is 300-600 times higher than that of contrast poplars, and under the coercion of submergence, the expression quality of the ThRap2.1 gene is increased by thousands times. Test proves that the ThRap2.1 gene is an important gene for responding coercion of submergence, and has an important application value in the field of forest genetic engineering.