In this paper, the hairy roots of T. wilfordii were used as the experimental material. Primers were designed based on the transcriptomic data of T. wilfordii roots. We cloned the two AP2/ERF transcription factors from T. wilfordii hairy roots using reverse transcription polymerase chain reaction (RTPCR), separately named TwAP2/ERF1(GenBank accession GAVZ01042389.1) and TwAP2/ERF2(GenBank accession GAVZ01016765.1). The TwAP2/ERF1 gene contained 525 bp open reading frame (ORF) which encoding 186 amino acids. The ORF of the TwAP2/ERF2 gene was 789 bp, which encoding 262 amino acids. Both genes encode proteins that were hydrophilic proteins. The phylogenetic analysis showed that TwAP2/ERF1 was highly similar with Vernicia fordii AP2/ERF (APQ47444.1) and Vernicia montana AP2/ERF(APQ47365.1). TwAP2/ERF2 was closely related to Populus trichocarpa AP2/ERF (XP_002304640.1) and Prunus pseudocerasus AP2/ERF(ALD84477.1). After methyl jasmonate (MeJA) treatment in T. wilfordii hairy roots, the relative expression of TwAP2/ERF1 gene was significantly increased and reached the highest level at 9 h, which was 16.77 times than the control expression. In the early stage MeJA inhibited the expression of TwAP2/ERF2 gene, but after 48 h the relative expression level increased. These results showed that TwAP2/ERF1 response positively MeJA induction in early stage and probably involve the regulation of secondary metabolites biosynthesis in T. wilfordii. These will provide the basis for elucidating the regulation of secondary metabolites biosynthesis and for using biotechnology to enhance the content of secondary metabolites in T. wilfordii.