Vertebrate development begins with the patterning of the body axis, which is one of the most significantevents during early embryonic development. Previous genetic evidences suggest that Wnt, bone morphogenic protein(BMP), Nodal, and fibroblast growth factor (FGF) signaling networks act together to control the complex morphogeneticcell movements, development of the three germ layers, and establishment of dorsal-ventral, anterior-posterior, and left-rightaxes. In this review, we focus on the molecular nature of dorsal-ventral patterning in the zebrafish embryo, including a briefintroduction of the dorsal organizer, the molecular mechanisms of the Wnt/ β-catenin signaling pathway in dorsal organizerformation, and the molecular mechanisms of BMP signaling in establishment of the dorsal-ventral axis. Finally, we discuss the future directions of dorsal-ventral patterning research.