In this paper,long-term changes of ephippia (or resting eggs) of Daphnia species in the sediments (0-36 cm) of Lake Junshan, the typical isolated lake from Poyang Lake, were studied. The ages of the 36 cm sediments at 1^# and 2^# sampling points are in 1839 and 1857, respectively. Before 1958, the accumulation rate of the sediment core in Junshan Lake showed a high level, but it obviously reduced after the dam was built in 1959. Before 1958, total nitrogen and total phosphorus contents in the sediments of Junshan Lake were relatively stable. However, the total nitrogen content showed obviously increasing trend after the dam was built. In the sediment of Junshan Lake, three Daphnia species (D. similoides sinensis, D. galeata and D. pulex) were identified. The accumulation rates and densities of both total ephippia and ephippia containing resting eggs in three Daphnia species showed a similar change pattern in the 1^# and 2^# sediments. Before 1958, the accumulation rates and densities of both total ephippia and ephippia containing resting eggs in three Daphnia species were at low levels (1^# sediment core:0-1.51×10³ ind./(m²·a) and 0-0.63 ind./(g·dw), 2^# sediment core:0-0.70×10³ ind./(m²·a) and 0-0.22 ind./(g·dw)). After the dam was built in 1959, the accumulation rates and densities of both total ephippia and ephippia containing resting eggs in three Daphnia species in the 10-1 cm sediments showed a gradual increasing trend, especially in the sediment layers of 3-1 cm (2009-2015). Pearson correlation showed that there were significant relationships between total nitrogen (TN) content and the accumulation rates of both total ephippia and ephippia containing resting eggs in three Daphnia species in the 1^# sediment score. There were significant relationships between TN and total phosphorus (TP) contents in the 2^# sediment core and the accumulation rates of total ephippia in three Daphnia species. Significant relationships between both TN and TP contents and the accumulation rates of ephippia containing resting eggs of D. similoides sinensis in the 2^# sediment core were also observed. The results suggested that long-term changes of the nutrient contents and ephippia (or resting eggs) of Daphnia species in the sediment core could reflect the historical evolution of eutrophication and Daphnia populations in lakes.