As a vertebrate genetic model, the zebrafish has been well recognized for its strength in studying a variety of biological processes and human diseases. Traditional forward genetic screens in zebrafish have generated a large pool of mutants with interesting phenotypes resembling human diseases but the underlying mechanisms are not well understood. A powerful approach to elucidate the mechanisms of these mutants is the modifier screen, which identifies 2(nd)-site mutations that specifically enhance or block the phenotype of a given mutant. Here we described the first genetic suppressor screen in zebrafish, which identifies a novel transcriptional mechanism regulating erythropoiesis. In combination with the haploid genetics in zebrafish, we have shown the feasibility and strength of a modifier screen in zebrafish. This strategy will greatly broaden the utility of the zebrafish as a model for making original discoveries and establishing novel paradigms for understanding vertebrate biology.