Long non-coding RNAs (lncRNAs) show patterns of tissue- and cell type-specific expression that are very similar to those of protein coding genes and consequently have the potential to control stem and progenitor cell fate decisions along a differentiation trajectory. To understand the roles that lncRNAs may play in hematopoiesis, we selected a subset of mouse lncRNAs with potentially relevant expression patterns and refined our candidate list using evidence of conserved expression in human blood lineages. For each candidate, we assessed its possible role in hematopoietic differentiation in vivo using competitive transplantation. Our studies identified two lncRNAs that were required for hematopoiesis. One of these, Spehd, showed defective multilineage differentiation, and its silencing yielded common myeloid progenitors that are deficient in their oxidative phosphorylation pathway. This effort not only suggests that lncRNAs can contribute to differentiation decisions during hematopoiesis but also provides a path toward the identification of functional lncRNAs in other differentiation hierarchies. Display omitted •Conserved differential expression of syntelogs to enrich functional lncRNAs•Bone marrow transplant of lncRNA-depleted HSCs uncovers in vivo functional lncRNAs•Spehd is required for differentiation during reconstitution and homeostasis•Myeloid progenitors depleted of Spehd show oxidative phosphorylation defects Delás et al. identify Spehd as an lncRNA expressed in hematopoietic stem and progenitor cells and required for in vivo differentiation during transplantation and homeostasis.