T cells develop in the thymus, where they acquire a range of distinct functional identities. T cells are divided into the αβ or γδ lineages. Progenitors that enter the thymus remain multipotent, with the potential to differentiate into a range of cell types. T lineage identity is then fixed early in T cell development. Later, γδ T cells branch off, while αβ development continues onto additional stages. Studies over the years have defined, at a population level, many of the specific genes that have to be activated or silenced as T cell progenitors differentiate toward either lineage. However, it is still unknown whether this combination of activation/silencing actually occurs in each and every cell as they differentiate. To investigate this, single-cell RNA-sequencing (scRNA-seq) was employed to re-assemble de novo a model of the early stages in T cell development based on the transcriptional profiles of individual cells. >20,000 CD4-CD8- double negative (DN) and γδ thymocytes were analysed using Chromium 10x scRNA-seq over three runs. Hierarchical clustering revealed that early thymocyte populations are much more complex than the standard view of T cell development. Assembly of these thymocyte populations into developmental trajectories based on gene expression suggested that the decision to differentiate into αβ versus γδ T cells occurs at a much earlier stage than the current model and that distinct DN1 and DN2 sub-populations are specific to either the αβ or γδ developmental pathways. To confirm that specific sub-populations are restricted to either αβ or γδ lineages, they were sorted and analysed for lineage outcomes in OP9-DL1 cultures. We show that lineage is already restricted in DN1 thymocytes, which is considered the earliest stages of T cell development. Thus, γδ developmental appears to occur in a parallel with αβ development and not a branch as previously thought.