Citron kinase (CIT-K) is a critical regulator of cytokinesis and neural development, and its deficiency in humans and mice leads to microcephaly and other neurodevelopmental defects (Bianchi et al., 2020). The zebrafish cita gene is the homolog of CIT-K. In this study, we employed the cita sa33521 nonsense mutant zebrafish as a model organism and analyzed the effects of the mutation on neural development using zHuC whole-mount in situ hybridization. The results showed that mutant embryos exhibited a reduction in midbrain neurons as early as 14 hours post-fertilization (hpf). During the critical neurodevelopmental period between 18 and 20 hpf, cells with abnormal cytokinesis likely underwent extensive apoptosis, resulting in a significant decrease in the zHuC-positive area within the midbrain region. At 22 hpf, a slight recovery in this area was observed, suggesting the activation of a compensatory mechanism. This study confirms that the cita gene plays an essential role in zebrafish neural development and that its loss of function leads to midbrain defects. Further investigation into the molecular mechanisms of cita and the potential pharmacological or genetic rescue pathways may provide insights into the pathogenesis and treatment of human microcephaly and related neurodevelopmental disorders.