Transcription factors (TFs) are pivotal in regulating gene expression, with the WRKY superfamily being prominent in plants. We explore the evolutionary landscape and functional diversity of WRKY TFs in two wild rice species, Oryza coarctata and Oryza nivara, compared to cultivated rice (Oryza sativa). Utilizing genomic data and computational methods, we identify WRKY TFs and analyze their phylogenetic relationships, revealing evolutionary patterns and similarities between the wild species and O. sativa. The WRKY TF family demonstrates extensive distribution across chromosomes, with specific clustering observed. Notably, O. coarctata and O. nivara exhibit distinct WRKY TF profiles despite their relatedness. Moreover, we uncover the regulatory networks associated with WRKY TFs, elucidating key genes and interactions involved in plant growth, development, and stress responses. Through network analysis, WRKY TFs emerge as central regulators, with WRKY71 notably regulating various stress responses in rice. Additionally, WRKY TFs like WRKY53, WRKY62, and WRKY28 are implicated in salinity stress and defense mechanisms, underscoring their multifaceted roles in plant adaptation. Furthermore, we investigate the structural features of hub genes, shedding light on their functional significance. Comparative protein structure analysis reveals conserved domains and structural similarities across wild and cultivated rice species, indicating evolutionary conservation in most of the genes, while in a few significant structural variations were observed. These findings offer valuable resources for further exploration of WRKY-mediated regulatory networks and genetic engineering strategies aimed at enhancing crop resilience and productivity in changing environments.