Exploration on aquatic microalgae in Sunter II Lake of North Jakarta and Agathis small Lake of Universitas Indonesia had been done in 2003, 2006, and 2012. Samples were taken on August 24, 2003; September 10, 2006; and September 20, 2012. The bluish-green color of the lake and scum on the water surface bring about hypothesis that Cyanobacteria were dominant in the lake. The aims of the research were to understand the composition of aquatic microalgae, and to know the dominant microalgae in Sunter II Lake and Agathis small Lake. The water samples were taken using plankton net (20 μm mesh) with horizontal tow. Environmental parameters to be measured were water temperature, light intensity, transparency, pH, DO and conductivity. The results showed that numbers of microalgae genera in Sunter II Lake and Agathis small Lake were between 10 and 15 genera. In Sunter II Lake, 15 genera were found in 2003, while 10 genera were found in 2006 and 2012. Meanwhile, in Agathis small Lake, 14 to 15 genera were found in 2006 and 2012. Those microalgae members were belong to four divisions, which are commonly found in lake waters, i.e. Chlorophyta, Cyanobacteria/Cyanophyta, Euglenophyta, and Chromophyta (class Bacillariophyceae/diatom). Among those four divisions, members of Cyanobacteria were not common but dominant. Three genera were found in 2003 (in Sunter II Lake) and 2012 (in Agathis small Lake), and two genera were found in 2003 (in Agathis small Lake), 2006 (in Sunter II Lake and Agathis small Lake), and 2012 (in Sunter II Lake). There was one genus of Cyanobacteria that dominant in the Sunter II Lake, i.e. Planktothrix or Planktothrix agardhii, with 89.5501% (2003), 53.4817% (2006), and 50.8839% (2012). Meanwhile, the abundance Planktothrix agardhii found in Agathis had increased over time, i.e. 16.5525% (2003); 25.9151% (2006); and 59.1502% (2012). Planktothrix agardhii is known as Cyanobacteria, which can produce harmful toxin. Because of that, the research on that dominant Cyanobacteria need to be done in more detailed to understand the toxicity and the influence of that Cyanobacteria to the lake condition, especially the changing of microalgae composition, and the influence to others organisms.