We have recently identified the p53-related DeltaNp63 gene as a transcriptional target of Bmp signaling that encodes a transcriptional repressor blocking neural development in the zebrafish ectoderm. However, in contrast to Bmps, the neural-repressing effect of forced DeltaNp63alpha expression is restricted to the presumptive forebrain, while posterior regions of the brain are not affected. Here, we show that this is due to instability of DeltaNp63alpha protein on the dorsal side of the embryo. In a yeast-two-hybrid screen, we isolated two DeltaNp63alpha-modifying enzymes, the SUMO-conjugating enzyme Ubc9 and the ubiquitin ligase Nedd4. The proteins bind to distinct sites in the C-terminal region of DeltaNp63alpha, which are absent in the shorter and more stable DeltaNp63gamma isoform. Similarly, mutant versions of DeltaNp63alpha unable to bind Nedd4 or Ubc9 are stabilized. DeltaNp63alpha is sumoylated and ubiquitinated both in HEK293 cells and in zebrafish embryos, and Nedd4 promotes ubiquitination and instability of DeltaNp63alpha protein, with lysine residue 637 serving as a potential alternative sumoylation and ubiquitination site that is crucial for DeltaNp63alpha destabilization. In zebrafish, ubc9.1 and nedd4 show restricted expression on the dorsal side of the embryo, where DeltaNp63alpha instability can be overcome upon blockage of endogenous Nedd4 activity, or upon injection of mutant versions of DeltaNp63alpha that are unable to bind Nedd4 or Ubc9. This results in a more widespread neural repression, affecting the entire Bmp-sensitive neuroectoderm. In sum, our data indicate that DeltaNp63alpha is ubiquitinated in a Nedd4- and sumoylated in a Ubc9-dependent fashion, and that these modifications can regulate DeltaNp63alpha stability in the zebrafish ectoderm.