Phoronida is a small phylum of benthic marine invertebrates that can occur in large numbers globally. The study of phoronid morphology and anatomy is important for understanding phoronid biology and the function of benthic communities dominated by phoronids. Because all phoronids are tube-living animals, the study of the morphology and ultrastructure of the body wall is an important step toward understanding the processes of the tube formation, growth, and renovation. This study used epoxy histology, scanning and transmission electron microscopy to describe the body regionalization and ultrastructure of the body wall epithelium of the unusual Phoronis embryolabi, which lives as a commensal in burrows of digging shrimps. The trunk of P. embryolabi consists of 8 zones, which are clearly distinguishable in living individuals. These zones are as follows: long head region, median sphincter with its three different parts (waist, upper and lower), muscular region, reproductive region, zone 7, and ampulla. Such body division can correlate with specificity of life style of P. embryolabi. The ultrastructure of the epithelium of all zones differ from each other in thickness, set and abundance of gland cells, structure of the extracellular matrix that underlies the epithelium, and abundance of neurites. The capacity and distribution of glandular cells correlate with tube formation and remodelling. Bacteria of two different types are described along body wall of all parts of the trunk; reciprocally advantageous phoronid-bacteria interaction is suggested. Our data suggest that P. embryolabi is able to build the tube at the anterior end rather than at the posterior end, as previously suggested for other phoronid species. At the same time, the certain mechanism of phoronid tube growth and remodelling is still unknown for phoronids as well as for many other tube-living invertebrates.