© 2020 Elsevier B.V. Although inquilinism in the goby–alpheid shrimp association is well known, behavior inside the burrow remains unclear because it is difficult to observe. In this tank study, alpheid shrimp burrow morphology was investigated because it may reflect the behavior of the burrow inhabitants. The objective was to elucidate the effects of Acentrogobius sp. 2 (sensu Akihito et al., 2013) on the burrow morphology of Alpheus brevicristatus. Through mesocosm experiments, 12 burrows made by shrimp without goby (solitary treatment), and 14 burrows made by shrimp with goby (symbiotic treatment), were recovered. Differences between solitary and symbiotic treatments were identified using a univariate test of each burrow parameters (total depth, total length, horizontal extension, diameter, number of openings, and number of side branches) and multivariate methods (nMDS and ANOSIM). Results indicate that the effect of the symbiotic goby on the shrimp burrow is small or smaller than the effect of shrimp size. However, the treatments varied significantly in terms of the correlation between shrimp size and each burrow parameter. In the solitary treatment, almost all the burrow parameters showed a high correlation with shrimp carapace length, suggesting that the burrow size was optimal for the shrimps. In contrast, no significant correlation was observed between most of the burrow parameters and shrimp size in the symbiotic treatment. Smaller burrows may not be suitable for the shrimp, and larger burrows require more energy to construct and maintain, suggesting that this relationship is costly to the shrimps. This study was carried out using the facultatively symbiotic goby–shrimp interaction, because the obligate shrimp is known to stop burrowing activity without the symbiotic goby. Future investigation using obligately symbiotic goby might lead to different results from those of this study, because the more specialized mutualist gobies will provide greater services to the shrimps. Studying the ecology of both obligate and facultative associations would provide further insight into the evolution of goby–alpheid shrimp symbiosis.