Apolipoprotein C1 (Apocl) is associated with lipoprotein metabolism, but its physiological role during embryogenesis is largely unknown. We reveal a new function of Apoclb, a transcript isoform of Apocl, in epiboly during zebrafish gastrulation. Apoclb is expressed in yolk syncytial layers and in deep cells of the ventral and lateral region of the embryos. It displays a ra- dial gradient with high levels in the interior layer and low levels in the superficial layer. Knockdown of Apoclb by injecting antisense morpholino (MO) caused the epiboly arrest in deep cells. Moreover, we show that the radial intercalation and the ra- dial gradient distribution of E-cadherin are disrupted both in Apoclb knockdown and overexpressed embryos. Therefore, Apoc 1 b controls epiboly via E-cadherin-mediated radial intercalation in a gradient-dependent manner.