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Echiurida is a group of marine benthic invertebrates, living in burrows and have hidden life style. Investigation of morphology and anatomy of all organ systems will help to understand the biology of echiurids, many of which are deep sea species. Morphology and microscopical anatomy of deep sea Protobonellia zenkevitchi Murina, 1976 were studied by methods of light microscopy and histology. The presence of ciliary grooves and vacuolated cells in connective tissue of the distal part of the proboscis allowed to suggest the specific position of the proboscis on the substratum and mechanism of sort of food particles. It was shown for the first time that the coelom is not subdivided into compartments: the united coelom occupies the proboscis and trunk. New segment of digestive tract, which probably functions for storage of food and for thorough digestion, was described for the first time. This portion of the digestive tract is important in oligotrophic conditions of deep sea. The circulatory system of P. zenkevitchi lacks of neuro-intestinal and ring blood vessels. The oocyte storage chamber of the gonoduct has a pore, which opens into the trunk coelom. Comparative analysis revealed that many organ systems in P. zenkevitchi have simpler organization in comparison with other echiurids. This simplicity may correlate with small body size of P. zenkevitchi and may be caused by living in deep sea. At the same time, P. zenkevitchi has some unique anatomical characteristics, which correlate with specific biology of this species. Work is supported by Russian Science Foundation (14-50-00029).