As a family of transcription factors, WRKY protein plays an important regulatory role in plant growth and development and in response to environmental signals. In this study, the whole genome data of pomegranate were used to systematically analyze the proteins’ physicochemical properties, phylogenetic evolution, gene structure, conserved motifs, cis-acting elements, protein interaction, gene co-expression, and transcriptome expression patterns of pomegranate WRKY transcription factors by bioinformatics. We identified 69 genes, PgWRKY gene group identification and evolutionary analysis show that WRKY proteins can be divided into Ⅰ, Ⅱ and Ⅲ altogether three types. Cis-acting element analysis showed that PgWRKY gene was widely involved in abiotic stress. Protein interaction network and co-expression analysis suggested that PgWRKY gene might play a consistent role in the same stress response and induce expression simultaneously. RNA-seq data analysis indicated that PgWRKY gene had certain tissue expression specificity and was widely involved in plant nutrition, reproductive growth and root stress response.