The transcription factor Zelda (Zld) is essential for zygotic genome activation in Drosophila embryo. It is maternally deposited and activates groups of pre-blastoderm genes required for sex determination, cellularization and embryonic patterning, either alone or in combination with other transcription factors. Zld is a large DNA binding protein (1596 aa) containing six predicted C2H2 type Zn finger domains. Two of them (ZF1, ZF2) are located in the N-terminal half of the protein, while the others are clustered close to the C-terminal end. Zld cognate binding sites, CAGGTAG and related sites (TAGteam sites), are enriched in the regulatory elements of its target genes. In vitro binding experiments have shown that the C-terminal Zn fingers are required for binding to DNA, but it is not known how each of them is involved in the binding. The function of the N terminal Zn fingers is unknown. Here we use in vitro mutagenesis and DNA binding assays (gel shifts and protein binding microarrays) to further characterize the functional properties of Zld’s Zn fingers. Surprisingly, we discovered a new DNA binding activity to G-rich sequences for ZF2 and adjacent conserved amino acids. We also quantified the contribution of the C-terminal cluster to the affinity and specificity of binding to different TAG team sites. We discuss the implications of these findings for Zld function in Drosophila embryos.