Populus lasiocarpa is a poplar species only locally distributed in China, and its growth and distribution range is seriously constrained by environmental factors such as drought and waterlogging. AP2/ERF transcription factor family plays important roles in response to abiotic stresses in plants. In this study, transcriptome sequencing, bioinformatics analysis and experimental validation were integrated to investigate genes that are likely to be involved in responses of drought and waterlogging stresses. The main results were presented as follows: (1) A total of 3,986 and 385 differentially expressed genes (DEGs) were detected under drought and waterlogging conditions respectively, of which 237 DEGs were shared under drought and waterlogging stresses. (2) A total of 205 AP2/ERF members were identified in P. lasiocarpa, which were clustered into five subfamilies and significantly enriched in DEGs. (3) Multiple PlAP2/ERF differentially expressed genes that are involved in the response of drought and waterlogging stresses were further confirmed by qRT-PCR. In conclusion, our results found that the number of DEGs under waterlogging stress were less than that under drought stress in P. lasiocarpa. PlAP2/ERF genes were highly involved in the process of abiotic stresses response.