Single-cell approaches have revealed that the haematopoietic hierarchy is a continuum of differentiation, from stem cell to committed progenitor, marked by changes in gene expression. However, many of these approaches neglect isoform level information, and thus do not capture the extent and effect of alternative splicing within the system. Here, we present the first integrated short- and long-read single-cell RNA-seq of haematopoietic stem and progenitor cells. We demonstrate that over half of genes detected in standard short-read single-cell analyses are expressed as multiple, often functionally distinct, isoforms. This includes many transcription factors and key cytokine receptors, and in particular the Thrombopoietin receptor Mpl, which displays complex isoform expression patterns between individual hematopoietic stem cells. The dataset further reveals novel signatures of hematopoietic ageing, including a global increase in lncRNA expression. Strikingly, the long-read sequencing enables us to observe aberrant expression of full-length VJ-rearranged immunoglobulin kappa transcripts in aged haematopoietic stem cells, prior to lymphoid commitment. Integrating single cell and cell-type specific isoform landscape in normal and aged hematopoiesis provides a new reference for accurate molecular profiling of heterogeneous tissues, as well as novel insights into transcriptional complexity, cell-type specific splicing events and effects of ageing.