A new bHLH gene from mouse that we call pMesogenin1 (referring to paraxial mesoderm-specific expression and regulatory capacities) and its candidate ortholog from Xenopus were isolated and studied comparatively. In both organisms the gene is specifically expressed in unsegmented paraxial mesoderm and its immediate progenitors. A striking feature of pMesogenin1 expression is that it terminates abruptly in presumptive somites (somitomeres). Somitomeres rostral to the pMesogenin1 domain strongly upregulate expression of pMesogenin's closest known paralogs, MesP1 and MesP2 (Thylacine1/2 in Xenopus). Subsequently, the most rostral somitomere becomes a new somite and expression of MesP1/2 is sharply downregulated before this transition. Thus, expression patterns of these bHLH genes, together with that of an additional bHLH gene in the mouse, Paraxis, collectively define discrete but highly dynamic prepatterned subdomains of the paraxial mesoderm. In functional assays, we show that pMesogenin1 from either mouse or frog can efficiently drive nonmesodermal cells to assume a phenotype with molecular and cellular characteristics of early paraxial mesoderm. Among genes induced by added pMesogenin1 is Xwnt-8, a signaling factor that induces a similar repertoire of marker genes and a similar cellular phenotype. Additional target genes induced by pMesogenin1 are ESR4/5, regulators known to play a significant role in segmentation of paraxial mesoderm (W. C. Jen et al., 1999, Genes Dev. 13, 1486-1499). pMesogenin1 differs from other known mesoderm-inducing transcription factors because it does not also activate a dorsal (future axial) mesoderm phenotype, suggesting that pMesogenin1 is involved in specifying paraxial mesoderm. In the context of the intact frog embryo, ectopic pMesogenin1 also actively suppressed axial mesoderm markers and disrupted normal formation of notochord. In addition, we found evidence for cross-regulatory interactions between pMesogenin1 and T-box transcription factors, a family of genes normally expressed in a broader pattern and known to induce multiple types of mesoderm. Based on our results and results from prior studies of related bHLH genes, we propose that pMesogenin1 and its closest known relatives, MesP1/2 (in mouse) and Thylacine1/2 (in Xenopus), comprise a bHLH subfamily devoted to formation and segmentation of paraxial mesoderm.