Several studies indicate that burrows play an essential role in burrowing fish, especially mudskippers, but little is known on burrow morphology and utilization of Periophthalmodon septemradiatus. This study was therefore conducted at five sampling sites from the estuary to upper reaches of Hau River to contribute to the knowledge of the behavior of Pn. septemradiatus, via in situ and ex situ observations of the utilization of burrow structures. Burrows made by polyester resin were used to determine their morphology. The male mudskippers Pn. septemradiatus were observed to excavate burrows using their mouths during the low tide. The burrows’ shapes were found to be J, U and W, with 1–3 openings and one bulbous chamber. The chamber was used as egg container where the mudskipper deposits their fertilized eggs. W-shaped burrows were found to be interconnected chambers where the mudskipper used it to change direction of movements inside the burrow. For the J- and U-shaped burrows, the commonality at all five sites was identified. The W-shaped burrows were common and were only found at two sites (Long Duc and An Lac Tay). For the burrows’ structure, the openings to the surface were oval, circular and bulbous in shape. Yet, there were variations between sites, and the burrows’ size was similar during the dry and wet seasons. At different sites, the depth of the burrows seasonally changed. The burrows used by mudskipper provide shelter, spawning sites, and access to feeding grounds for other mudskipper species.