BackgroundWRKYtranscription factors are a prominent gene family in plants, playing a crucial role in various biological processes including development, metabolism, defense, differentiation, and stress response. Although theWRKYgene family has been extensively studied and analysed in numerous plant species, research onPrunus sibirica’sWRKYgenes (PsWRKY) remains lacking.ResultsThis study analysed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, and Gene ontology (GO) annotation ofPsWRKYgene family members using bioinformatics methods based on the whole-genome data ofP. sibirica. In total, 55WRKYswere identified inP. sibiricaand were heterogeneously distributed on eight chromosomes. Based on the phylogenetic analysis, theseWRKYswere classified into three major groups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Members of different subfamilies have different cis-acting elements, conserved motifs, and intron-exon structures, indicating functional heterogeneity of theWRKYfamily. Prediction of subcellular localisation indicated thatPsWRKYswere mainly located in the nucleus. Twenty pairs of duplicated genes were identified, and segmental duplication events may play an important role inPsWRKYgene family expansion. Analysis of the Ka/Ks ratio showed that thePsWRKYfamily’s homologous genes were primarily purified by selection. Additionally, GO annotation analysis showed that theWRKYgene family was mainly involved in responses to stimuli, immune system processes, and reproductive processes. Furthermore, quantitative real-time PCR (qRT-PCR) analysis showed that 23PsWRKYswere highly expressed in one or more tissues (pistils and roots) andPsWRKYsshowed specific expression patterns under different low-temperature stress conditions.ConclusionsOur results provide a scientific basis for the further exploration and functional validation ofWRKYsinP. sibirica.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09469-0.