Brachiopods are benthic marine invertebrates that live enclosed in a bivalved shell. Despite having a reduced and unsegmented trunk in the adult stage, brachiopod larvae show putative segmented structures such as transverse ectodermal boundaries and iterated coelomic sacs. Several molecular mechanisms of segmentation have been described in animals considered to be segmented (i.e., the distantly related annelids, arthropods and vertebrates), but far less is known about the role of these "segmentation genes" in other organisms. Here we investigate the expression of the arthropod segment polarity genes engrailed, wnt1 and hedgehog in the development of brachiopods—a group more closely related to the segmented annelids. Expression of engrailed correlates with the development of an anterior nonsegmental ectodermal boundary in the embryos of Terebratalia transversa and Novocrania anomala. Surprisingly, wnt1 is expressed as a stripe adjacent to engrailed in T. transversa in the same manner as in the parasegment boundaries of insects. Expression of hedgehog, however, is restricted to the endoderm and is not compatible with a segment polarity role. In addition, the putative engrailed regulators pax6 and pax2/5/8 encircle the whole embryo and demarcate this anterior ectodermal boundary before engrailed. We conclude brachiopod larvae might have a common anterior patterning involving the expression of pax6, pax2/5/8 and engrailed. Despite key differences to other segment boundaries (e.g., hedgehog expression), we show the characteristic adjacent stripes of engrailed and wnt1 can occur in a nonsegmental ectodermal boundary. A comparison among bilaterians suggests the ancestral expression of engrailed during early development was nonsegmental and conceivably related to the embryonic head/trunk boundary. Our data implies that engrailed was independently recruited to the segment boundaries of annelids and arthropods and to other different developmental boundaries during evolution.