The lateral line is a mechanosensory system in fish and amphibians to detect local water flow and pressure. Development of the posterior lateral line (PLL) originates from the migrating PLL primordium (PLLP). The PLLP deposits neuromasts on the trunk during migration to the tail. Molecular dissection revealed that PLL development is associated with genes mediating cell adhesion, morphogenesis, neurogenesis and development, but the regulatory signaling network is far from completion. To further investigate candidate regulatory genes for lateral line development, we found using whole-mount in situ hybridization that calnexin, an endoplasmic reticular (ER) calcium-binding protein gene, is expressed in PLL neuromasts. Knockdown of calnexin using antisense morpholino oligonucleotides resulted in a dose-dependent reduction in neuromasts and hair cells of the PLL. Using a transgenic claudin b:gfp line, we observed a notably reduced PLLP size, but no significant migration defect in calnexin morphants. Finally, we discovered that the reduced PLLP is associated with a reduction in cell proliferation and an increase in ER stress-dependent apoptosis. These results suggest that calnexin is essential for neuromast formation during lateral line development in the zebrafish.