Transcription of the CYBB gene, which encodes the respiratory burst oxidase protein, gp91phox, is restricted to phagocytic cells, differentiated beyond the promyelocyte stage. Regulation of CYBB transcription involves several repressor cis elements in the promoter. These repressor elements are homologous to the derived consensus sequence for DNA-binding of HoxA10 as a hetero-dimer with Pbx1a. The HoxA10/Pbx1 complex recruits histone deacetylase 2 and represses CYBB transcription in undifferentiated cells. During myeloid differentiation, HoxA10 is tyrosine phosphorylated, which decreases DNA-binding affinity for the CYBB repressor element. In our previous investigations, we found this decreased binding affinity requires phosphorylation of two tyrosine residues in the DNA-binding homeodomain. These residues are highly conserved with other HoxA proteins. However, we also found decreased DNA-binding requires interaction of these homeodomain tyrosines with a non-conserved domain, amino terminal in HoxA10. In previous investigations, we determined these CYBB repressor cis elements function as positive cis elements in differentiated myeloid cells, and interact with an unidentified protein complex. In these studies, we investigate the proteins involved in transcriptional activation of the CYBB gene, via these promoter sequences. We find this cis element is activated by HoxA9 and Pbx1a, in differentiating myeloid cells. Consistent with this, we find increased binding of HoxA9 to this CYBB cis element, during myeloid differentiation, in vitro and in vivo. Consistent with our results with HoxA10, we find HoxA9 is tyrosine phosphorylated during myeloid differentiation. However, in contrast to HoxA10, we find tyrosine phosphorylation of the conserved residues in the HoxA9 DNA-binding homeodomain increases binding to the CYBB cis element. Therefore, we conclude HoxA10 and HoxA9 have opposing functions, for myeloid specific gene transcription, during differentiation. We also find these functions are regulated by post translational modification of conserved tyrosine residues in the homeodomain regions of these proteins. Additionally, our results suggest differences in the effect of phosphorylation of these residues on DNA-binding is likely due to interaction with non-conserved domains in HoxA9 and HoxA10.