The Wnt pathway is a highly conserved signal transduction pathway that plays many critical roles in early animal development. Recent studies have shown that this pathway plays a conserved role in the specification and patterning of the animal - vegetal (A - V) axis in sea urchins and sea anemones. These observations have suggested that the common ancestor to cnidarians and bilaterians used the Wnt signaling pathway for specifying and patterning this maternally established axis. Because the A - V axis plays a critical role in germ layer segregation, a better understanding of how the Wnt pathway is regulated along the A - V axis will provide key insight into the molecular mechanisms regulating germ layer segregation and germ layer evolution in animal embryos. Here, we provide a detailed protocol for using mRNA microinjection that can be used to analyze Wnt signaling in early sea urchin embryos. This protocol can also be adapted to introduce morpholino anti-sense oligonucleotides into sea urchin embryos.