Uranouchi Bay, an enclosed bay in the southern part of Shikoku Island, southwest Japan, has a complicated geography, being long and narrow with some small inlets. Since 1955, it has been influenced by organic pollution from fish farming. In the spring of 1954, many surface sediment samples were collected in the bay, and were then studied by Ishizaki (1968) to examine ostracode thanatocoenoses. Comparison with this earlier work allows us to investigate faunal changes over this approximately 50-year period. We collected surface sediment and seaweed samples in the bay for ostracode analysis in 2002 and 2005. A total of 124 species were obtained from 29 samples. Comparison between the results suggests that ostracodes have decreased in number in the inner part of the bay and increased greatly in the middle and outer parts of the bay. The number of species and the species diversity has also increased in the middle and outer parts of the bay. Mud dwellers have mostly disappeared from the inner bay and are now found in small inlets in the middle and outer parts of the bay. These changes are caused by the enlargement of areas of anoxic or oxygen-poor bottom waters in the inner part of the bay during the summer. This summer hypoxia is thought to have been brought on by organic pollution from fish farms and the complicated geographical features of the bay. The decrease of inflows of coarse-grained sandy sediments from the outside of the bay, resulting from the intermittent construction of artificial concrete banks in the mouth of the bay in 19461950, 19691974 and 19911996, induced the emergence of preferable environments for a variety of bay and phytal ostracodes in the middle and outer parts of the bay. Valves of phytal species such as xestoleberidid and paradoxostomatid ostracodes increased greatly in the muddy bottoms of the middle part of the bay, where many artificial floating rafts for fish farms are distributed. Seaweed has grown on submerged parts of the floating materials, providing new habitats for phytal ostracodes.