Some fish species living in mudflats construct burrows for dwelling and hiding. The goby Parapocryptes serperaster is a burrowing fish in mudflats of many estuaries in South East Asia. This study was carried out in the Mekong Delta, Vietnam, to examine burrow morphology and usage by this species. Morphology of the burrows constructed by P. serperaster was investigated by resin castings in situ to obtain the physical structure and configuration of each burrow. Fish from the burrows were caught and measured before burrow casts were made. Fish burrows comprised several openings, a few branching tunnels and multi-bulbous chambers. The surface openings were circular, and the shapes of branching tunnels were nearly round. The burrows had interconnected tunnels, and various short cul-de-sac side branches. The burrow structure differed between fish sizes but burrow dimensions were positively correlated with fish size, indicating that larger fish can make larger and more sophisticated burrow. The burrow structure and dimensions were not different between dry and wet seasons. The laboratory observations showed that P. serperaster used body movements to dig burrows in the sediment. Burrows could provide a low tide retreat and protection from predators, but were not used for spawning and feeding for this goby species. This study indicates that the burrowing activity of gobies is an important adaptation for living in shallow and muddy habitats.