The mudskipper Boleophthalmus pectinirostris maintained territories in farming ponds during the cold season between November and February. There were two types of territory, one was surrounded by mud-walls, and the other was without mud-walls. Both types of territory were entirely covered by shallow water. The area of walled territories was significantly bigger than that of non-walled ones. The nearest neighbour distance of walled territories was significantly shorter than that of non-walled territories. In January, fish surface activity occurred between 1200 and 1500 hours at which time the territorial water temperature reached a maximum, being significantly higher than that of the air, mud surface or deep burrow. The territorial sediments exhibited a significantly greater benthic microalgal biomass (chlorophyll-a and total chlorophyll-a) as compared to the non-territorial sediments. The present study indicates that B. pectinirostris forms a territory during the cold season to keep a pool of water that encourages diatom growth and enables the fish to engage in surface activity.