Celery (Apium graveolens L.) is rich in nutrient substances and is cultivated worldwide. WRKY protein family is one of the largest transcription factor families in plants and is involved in growth and development, signal transduction, senescence and stress resistance. In this study, we identified 69 celery WRKY family transcription factors based on conserved WRKY domain sequence from the celery genomic and transcriptomic data. Phylogenetic analysis of celery and Arabidopsis WRKY proteins divided these celery WRKY proteins into three groups, seven subgroups. The numbers of WRKY proteins in celery and other 16 species were compared to illustrate the evolution of WRKY transcription factors in plants. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyse the expression profiles of five selected AgWRKY genes under abiotic stress (abscisic acid, cold, drought and salt) treatments. The qRT-PCR results indicated that those selected AgWRKY family genes were upregulated under abiotic stress treatments. This study provides a basic research for further investigation of the structure and function of AgWRKY genes.