A bone morphogenetic protein (BMP) signaling pathway is implicated in dorsoventral patterning inXenopus.Here we show that three genes in the zebrafish,swirl, snailhouse,andsomitabun,function as critical components within a BMP pathway to pattern ventral regions of the embryo. The dorsalized mutant phenotypes of these genes can be rescued by overexpression ofbmp4, bmp2b,an activated BMP type I receptor, and the downstream functioningSmad1gene. Consistent with a function as a BMP ligand,swirlfunctions cell nonautonomously to specify ventral cell fates. Chromosomal mapping ofswirland cDNA sequence analysis demonstrate thatswirlis a mutation in the zebrafishbmp2bgene. Interestingly, our analysis suggests that the previously described nonneural/neural ectodermal interaction specifying the neural crest occurs through a patterning function ofswirl/bmp2bduring gastrulation. We observe a loss in neural crest progenitors inswirl/bmp2bmutant embryos, whilesomitabunmutants display an opposite, dramatic expansion of the prospective neural crest. Examination of dorsally and ventrally restricted markers during gastrulation reveals a successive reduction and reciprocal expansion in nonneural and neural ectoderm, respectively, insnailhouse, somitabun,andswirlmutant embryos, withswirl/bmp2bmutants exhibiting almost no nonneural ectoderm. Based on the alterations in tissue-specific gene expression, we propose a model wherebyswirl/bmp2bacts as a morphogen to specify different cell types along the dorsoventral axis.