Copper is an essential trace metal for physiological functions, whereas copper overload causes cytotoxicity in living organisms. Genetically determined systems regulate acquisition, distribution and storage for copper maintenance and homeostasis. The Human ATP7A copper transport ATPase modulates intracellular copper distribution, which is critical for copper-dependent enzymes such as superoxide dismutase (SOD1). To investigate the role of zebrafish ATP7A in copper homeostasis, zebrafish atp7a gene expression was reduced for analysis of downstream cellular function. The results demonstrated that zebrafish sod1 has lower expression in atp7a-knockdown fish. Similarly, zebrafish sp1, a transcriptional regulator of sod1, also shows reduced expression in atp7a-knockdown fish. The lower expression of sod1 resulting from atp7a knockdown is independent to p53 gene activation. The knockdown of atp7a and copper chelator NeoC results in hypopigmentation and notochord deformation in zebrafish. Addition of exogenous copper alleviated the impaired development. Interestingly, both sod1 and sp1 transcripts are reduced in the presence of NeoC and increased with exogenous copper, suggesting that the expression of sod1 and sp1 are directly affected by copper status. This is the first report to demonstrate a hierarchic gene expression of copper homeostatic genes between atp7a, sp1 and sod1 in zebrafish.