As one of the human activities that transform nature, construction of dams and dykes may impose significant effects on lake ecosystems. Due to lacking of comparative data for ecological monitoring, how the changes of phytoplankton community structure respond to altered hydrological connectivity between lakes and other water bodies is still unknown. This work chose Junshan Lake, the typical isolated lake from Poyang Lake floodplain, to investigate the succession in phytoplankton communities responding to altered connectivity. Phytoplankton samples were collected during the wet and dry seasons in Junshan Lake, to analyze the phytoplankton community structure. The results showed that, fifty three genera from six phyta were identified in Junshan Lake, with Chlorophyta (47.2%), Bacillariophyta (22.2%), Cyanophyta (14.8%) and Euglenophyta (9.3%) being the main phyta. The dominant species were Ceratium hirundinella (20.5%), Anabeana spp. (18.5%) and Microcystis spp. (12.9%) during the wet seasons. Cryptomonas ovate (38.4%), Aulacoseira granulata (15.2%) and Microcystis spp. (10.5%) dominated during the whole dry seasons. The total phytoplankton abundance was mainly composed of Cyanophyta (85.4% -87.0%). The total phytoplankton biomass was dominantly made up of Cyanophyta (45.0%), Dinophyta (21.1%), Bacillariophyta (15.6%) and Chlorophyta (11.5%) during the wet seasons. Cryptophyta (38.2%), Bacillariophyta (31.3%) and Cyanophyta (21.1%) were the main contributors of the total phytoplankton biomass during the dry seasons. The phytoplankton community structure changed from Dinophyta-Bacillariophyta type during the wet seasons of 2007-2008 to Cyanophyta- Dinophyta type during the wet seasons of 2012-2013, and changed from Dinophyta- Bacillariophyta type during the dry seasons of 2007-2008 to Cryptophyta- Bacillariophyta- Cyanophyta type during the dry seasons of 2012-2013. The abundance and biomass increased from 2.66 x 10(6) cell L(-1) during 2007-2008 to 6.77 x 10(7) cell x L(-1) during 2012- 2013, and from 0.72 mg x L(-1) during 2007-2008 to 12.30 mg x L(-1) during 2012-2013, respectively. The succession pattern of phytoplankton community in the Junshan Lake showed a decrease in the proportion of oligotrophic species as Chrysophyta and Dinophyta, and an increase in eutrophic species as Cyanophyta and Cryptophyta. Thus, being isolated from Poyang Lake might alter hydrologic factors so that the water exchange time became longer and the water flow became slower which could promote the growth and aggregation of phytoplankton eutrophication indicator species in Junshan Lake.