Hox and ParaHox genes are transcriptional regulators vital for many aspects of embryonic development in bilaterian animals and are considered to have originated from one ancestral proto-Hox/ParaHox cluster. Hox genes are clustered in the genome of both protostomes and deuterostomes, and there is a specific relationship between the position of a gene in the cluster and the position of its expression along the animal body axis (colinearity). It is not clear whether the ParaHox genes Gsx, Xlox, and, Cdx generally exhibit a similar phenomenon since developmental expression for all three ParaHox genes within a single species has not yet been described for any protostome animal. Here we show the spatial and temporal localization for all three ParaHox genes in the polychaete Capitella sp. I, a member of one of the morphologically most diverse and understudied groups within the Metazoa, the Lophotrochozoa. Our data demonstrate that although both CapI-Xlox and CapI-Cdx are regionally expressed in the gut, the three Capitella sp. I ParaHox genes as a group do not perfectly fit predictions of temporal or spatial colinearity. Instead, there is a conservation of expression across species associated with development of particular tissues, and the relative order of initiation of ParaHox gene expression likely reflects the relative order of species-specific tissue development during ontogenesis.