Coastal tide pools in southern Japan are inhabited by the rock-boring sea urchin Echinostrephus molaris, which excavate pits in the substrate. These pits are subsequently used by non-boring sea urchins such as Anthocidaris crassispina and Echinometra sp. B, and the recolonized pits are often inhabited by a commensal limpet-like trochid snail species, Broderipia iridescens. We explored the population and community dynamics of these sea urchins and the limpet-like snail by monitoring occupancy of 512 pits in tide pools in Shirahama, Japan from May 2017–May 2019. Initially, nearly all pits were occupied by any one of the three sea urchin species, but an unusual cold event in February 2018 caused a mass die off of these sea urchins. After this event, occupancy decreased from 99% to 15%, and the tropical species Echinometra sp. B disappeared from the study pools. We observed slow population recovery of E. molaris and A. crassispina, provably via migration of sub-adults from the subtidal zone. Turnover rate of the pit-occupying sea urchin species was <1.0% before the cold event, but drastically increased after the cold event. Population size of the commensal snail decreased along with those of their host, but the rate of commensalism was constant at 50–55% throughout the study period, suggesting that these snails followed their host sea urchins repeating inter-pit migration. Despite mass mortality and slow recovery, the sea urchin density remained high enough to maintain persistent sea urchin barrens throughout the study period.