Recent advances in single-cell transcriptomics techniques have opened the door to the study of gene regulatory networks (GRNs) at the single-cell level. Here， we studied the GRNs controlling the emergence of hematopoietic stem and progenitor cells from mouse embryonic endothelium using a combination of single-cell transcriptome assays. We found that a heptad of transcription factors (Runx1， Gata2， Tal1， Fli1， Lyl1， Erg and Lmo2) is specifically co-expressed in an intermediate population expressing both endothelial and hematopoietic markers. Within the heptad， we identified two sets of factors of opposing functions: one (Erg/Fli1) promoting the endothelial cell fate， the other (Runx1/Gata2) promoting the hematopoietic fate. Surprisingly， our data suggest that even though Fli1 initially supports the endothelial cell fate， it acquires a pro-hematopoietic role when co-expressed with Runx1. This work demonstrates the power of single-cell RNA-sequencing for characterizing complex transcription factor dynamics.