Studies implicate an important role for the mixed lineage leukemia (Mll) gene in haematopoiesis, mainly through maintaining Hox gene expression. However, the mechanisms underlying Mll-mediated haematopoiesis during embryogenesis remain largely unclear. Here, we investigate the role of mll during zebrafish embryogenesis, in particular, haematopoiesis. Mll depletion caused severe defects in haematopoiesis as indicated by a lack of blood flow and mature blood cells as well as a significant reduction in expression of hematopoietic progenitor and mature blood cell markers. Furthermore, mll depletion prevented the differentiation of hematopoietic progenitors. In addition, we identified the N-terminal mini-peptide of Mll acted as a dominant negative form to disrupt normal function of mll during embryogenesis. As expected, mll knockdown altered the expression of a subset of hox genes. However, overexpression of these down-regulated hox genes only partially rescued the blood deficiency, suggesting that mll may target additional genes to regulate haematopoiesis. In the mll morphants, microarray analysis revealed a dramatic up-regulation of gadd45αa. Multiple assays indicate that mll inhibited gadd45αa expression and that overexpression of gadd45αa mRNA led to a phenotype similar to the one seen in the mll morphants. Taken together, these findings demonstrate that zebrafish mll plays essential roles in haematopoiesis and that gadd45αa may serve as a potential down-stream target for mediating mll function in haematopoiesis.