Invariant natural killer T cells (iNKT cells) have immune stimulatory or inhibitory effects on the immune response that are context-dependent.  This may be attributed in part to the existence of functional iNKT cell subsets dedicated to producing certain cytokines, however, these subsets have only been characterized on the basis of differential expression of a few molecules.  Here we have undertaken a global analysis of gene expression in mouse thymic iNKT cell  subsets.  Cells were purified by sorting based on surface markers into NKT1, NKT2, and NKT17 cells and analyzed by RNA-Seq.  We also carried out single cell RNA-Seq of >40 cells from each population, and we have analyzed each population  by ChIP-seq for H3K27ac, a mark for active enhancers.  Our data indicate that the thymic iNKT cell subsets are highly and nearly equally divergent from one another, with more than 200 gene expression differences.  The differences include expression of transcripts encoding chemokines and integrins, suggesting the subsets localize differently, transcription factors, signaling molecules, cell cycle control, and different types of inhibitory receptors, which likely help to control their autoreactivity.  Transcripts encoding proteins potentially involved in anti-microbial effector functions also differ.  The single cell RNA-Seq demonstrated the purity of the populations, but also provided evidence for a surprising degree of heterogeneity within each subset.   The epigenetic analysis allowed us to predict transcription factors important for each subset and to identify a region in the Il4 locus uniquely marked in NKT2 cells. Deletion of this enhancer element caused a dramatic decrease in the ability of iNKT cells to produce IL-4 in vivo.  In summary, despite their restricted TCR diversity, the thymus imprints innate-like iNKT cells into subsets with novel combinations of properties that were not previously anticipated, indicating differences in proliferative capacity, homing, TCR signaling and effector function.