We investigated the estuarine goby's (Eutaeniichthys gilli) utilization of mud shrimp (Upogebia yokoyai) burrows in laboratory experiments at Kochi, Japan. The goby utilized the shrimp burrow in the presence of the host, without predators, when the mud surface was covered with water. The goby spent one quarter to half the time in shrimp burrows in experimental tanks. The goby frequently entered and exited the shrimp burrows, with bout durations of several seconds to several minutes. The goby also utilized vacant artificial burrows in much the same manner. It is suggested that E. gilli feeds on small-sized crustaceans and other organic matter on the mud surface frequently utilizing shrimp burrows for possible predator avoidance even when no predator is present. Repeated evolution of burrow utilization in the North Pacific bay gobies in both the East and West Pacific would correlate with burrow commensalism in E. gilli, which is the most proximal outgroup of the bay gobies.