Plant roots continuously grow, a unique features that gives them the opportunity to explore the soil for nutrients and water. Stem cells, located in the root tip meristem, ensure a continuous supply of different type of cells for root growth. Despite the identification of important pathways in seed plants, it is still an unresolved mystery how stem cell identity or differentiation is controlled and maintained. Furthermore, the complexity of the root meristem in seed plants, including different types of stem cells, complicates its research. In contrast to seed plants, earlier diverged plant lineages, ferns and lycophytes, have roots with only one stem cell and a less complex meristem. Their currently unknown mechanisms in the control of stem cells and differentiation are partially ancestral to these of seed plants, and could give insights in how root stem cell control evolved. A for plant science emerging technique, i.e. single cell RNAseq, provides an unprecedented resolution in gene expression patterns and open the way to discover key developmental regulators that control cell fate into distinctive cell shapes and functions. We therefore strongly believe that the momentum has come to apply scRNAseq on lycophyte and fern roots to identify the minimal, or possibly alternative requirements for stem cell fate or type-specific differentiation.