The WUSCHEL-RELATED HOMEOBOX 5 (WOX5) gene encodes the transcription factor, which is one of the key regulators maintaining the structure and functioning of the stem cell niche in plant root tips. WOX5 is expressed in the quiescent center of the root apical meristem, preventing the differentiation of the columella initials and, together with SCR, SHR, PLT1, and PLT2, participating in controlling the differentiation of other initials of the root meristem. However, the details of the WOX5 functioning are unclear. The WOX5 protein belongs to the WUSCHEL-related homeobox (WOX) family, the founder of which is the transcription factor WUSCHEL (WUS), maintaining the stem cell niche in the shoot apical meristem. WOX5 and WUS diverged from a common ancestor at the base of angiosperms, which resulted in a specialization of the shoot and root stem cell niches. However, the WOX5 structural and functional divergence during angiosperm evolution has been poorly addressed. In this review we present a systems biology analysis of the WOX5 gene to reveal specific features of its evolution and functioning. For this, we performed a phylogenetic analysis on 62 publicly available WOX5 amino acid sequences, integrated published data about WOX5 expression domain in Arabidopsis and other species and its role in development, and summarize the results of experiments on primary and secondary targets for this transcription factor. The data on the possible mechanisms of direct and indirect regulation of WOX5 expression were discussed. In particular, we analyzed the WOX5 promoter regions from 30 species. Possible direct regulators of WOX5 gene expression were proposed based on the presence of putative binding sites for the candidate transcription factors in the conserved WOX5 promoter regions.