Zebrafish erythropoietin a (epoa) is a well characterized regulator of red blood cell formation. Recent morpholino mediated knockdown data have also identified being essential for physiological pronephros development in zebrafish, which is driven by blocking apoptosis in developing kidneys. Yet, zebrafish mutants for have not been described so far. In order to compare a transient knockdown vs. permanent knockout for in zebrafish on pronephros development, we used CRISPR/Cas9 technology to generate knockout zebrafish mutants and we performed structural and functional studies on pronephros development. In contrast to morphants, zebrafish mutants showed normal pronephros structure; however, a previously uncharacterized gene in zebrafish, named , was identified and upregulated in mutants. knockdown altered pronephros development, which was further aggravated in mutants. Likewise, and morphants regulated similar and differential gene signatures related to kidney development in zebrafish. In conclusion, stable loss of during embryonic development can be compensated by leading to phenotypical discrepancies in knockdown and knockout zebrafish embryos.