The slit diaphragm (SD) is a highly specialized intercellular junction between podocyte foot processes and is crucial in the formation of the filtration barrier in the renal glomeruli. Zebrafish Nephrin and Podocin are important in the formation of the podocyte SD and mutations in NEPHRIN and PODOCIN genes cause human nephrotic syndrome. In the present study, the zebrafish Podocin protein was observed to be predominantly localized in the pronephric glomerular podocytes, as previously reported for Nephrin. To understand the function of Podocin and Nephrin in zebrafish, splice‑blocking morpholino antisense oligonucleotides were used. Knockdown of Podocin or Nephrin by this method induced pronephric glomerular hypoplasia with pericardial edema. Human Nephrin and Podocin mRNA rescued this glomerular phenotype, however, the efficacy of the rescues was greatly reduced when mRNA‑encoding human disease‑causing NEPHRIN‑R1109X and PODOCIN‑R138Q were used. Furthermore, an association between zebrafish Nephrin and Podocin proteins was observed. Notably, Podocin‑R150Q, corresponding to human PODOCIN‑R138Q, markedly interacted with Nephrin compared with wild‑type Podocin, suggesting that this strong binding capacity of mutated Podocin impairs the transport of Nephrin and Podocin out of the endoplasmic reticulum. The results suggest that the functions of Nephrin and Podocin are highly conserved between the zebrafish pronephros and mammalian metanephros. Accordingly, the zebrafish pronephros may provide a useful tool for analyzing disease‑causing gene mutations in human kidney disorders.