The burrow morphology of the mud shrimp Upogebia yokoyai was investigated on a tidal flat in the Nanakita River mouth in north-eastern Japan using in situ resin casting. A total of 26 burrow casts were recovered, including those of 16 large shrimps and 10 small shrimps. Burrows of large shrimp were relatively simple and Y-shaped with depth exceeding 1.2 m. Although burrow diameter was related to shrimp size, correlation with other burrow measurements was low. Three large casts were connected to others via a narrow horizontal portion potentially reflecting mating behaviour of the shrimp. Burrows of small shrimp were more complex than those of the other upogebiids and were connected to large burrows. In 6.7% of cases, bopyrid isopods were present in the branchial chamber. Three species of gobies were found in the burrows. These data show that burrows of U. yokoyai serve not only as a recruitment site for conspecific shrimp, but also as habitat for other animals in the tidal flat.