Tsunamis associated with the 2011 off the Pacific Coast of Tohoku Earthquake seriously disrupted the shallow marine ecosystem along a 2000 km stretch of the Pacific coast of Japan. The effects of the 2011 tsunamis on the soft-bottom benthic community have been relatively well studied in the intertidal zone, whereas tsunami effects on the subtidal benthos remain poorly understood. Here, we investigated populations of the world’s largest spoon worm Ikeda taenioides (Annelida: Echiura: Ikedidae) in subtidal zone of Funakoshi Bay, Tohoku District, northeastern Japan. Subtidal scuba-diving surveys at two sites in the bay showed extremely long proboscises frequently extending from small holes in the sandy seafloor shortly before and soon after the tsunami disturbances. Based on morphological and molecular identification, the proboscises were revealed to be parts of I. taenioides. On 30 November 2011, 265 days after the tsunami event, many large-sized individuals with >1 m long proboscises were observed; these individuals were probably not derived from post-tsunami larval recruitment but more likely survived the tsunami disturbances. This is surprising because other sympatric megabenthos (e.g. spatangoid echinoids and venerid bivalves) and seagrass beds were almost completely destroyed (although they later recovered) by the tsunamis in this bay. The burrows of I. taenioides are known to be very deep (70–90 cm), which may have sheltered them from the impacts of the tsunamis. Our observations suggest that the effects of the 2011 tsunamis on benthos in soft sediments may differ depending on their burrowing depth.