The origin of chordates remains one of the major puzzles of zoology, even after more than a century of intense scientific inquiry, following Darwin's “Origin of Species”. The chordates exhibit a unique body plan that evolved from a deuterostome ancestor some time before the Cambrian. Molecular data gathered from phylogenetics and developmental gene expression has changed our perception of the relationships within and between deuterostome phyla. Recent developmental gene expression data has shown that the chordates use similar gene families and networks to specify their anterior-posterior, dorsal-ventral and left-right body axes. The anterior-posterior axis is similarly established among deuterostomes and is determined by a related family of transcription factors, the Hox gene clusters and Wnt signaling pathways. In contrast, the dorsal-ventral axis is inverted in chordates, compared with other nonchordate invertebrates, while still determined by expression of BMP signaling pathway members and their antagonists. Finally, left-right asymmetries in diverse deuterostomes are determined by nodal signaling. These new data allow revised, testable hypotheses about our earliest ancestors. We present a new hypothesis for the origin of the chordates whereby the expansion of BMP during dorsal-ventral patterning allowed the evolution of noneural ectoderm and pharyngeal gill slits on the ventral side. We conclude that “Man is but a worm…,” that our chordate ancestors were worm-like deposit and/or filter feeders with pharyngeal slits, and an anterior tripartite unsegmented neurosensory region. genesis 46:605–613, 2008. © 2008 Wiley-Liss, Inc.