The distribution of bloom-forming cyanobacteria in eutrophic to hypereutrophic ponds was studied in northern Taiwan in 2009. Eighty-four ponds were sampled in mid-summer, and the relationship between colony size and relative abundance of each cyanobacterial species was analyzed. Anabaena crassa and Cylindrospermopsis raciborskii were the dominant species in terms of frequency of appearance. The colony size of An. crassa increased significantly with its relative abundance. The relative abundance of C. raciborskii was usually below 10%, and its filament length was not correlated with its relative abundance. The colonies of Microcystis aeruginosa normally consisted of several tens of cells. However, when M. aeruginosa exclusively dominated the plankton community, the average number of cells in a colony reached several hundreds. The mean filament length of Planktothricoides raciborskii significantly increased with its relative abundance. The correlations between colony size and relative abundance of the ten cyanobacterial species were significantly positive for three species, insignificantly positive for five species and insignificantly negative for two species. Given the various ecological advantages of large colonies, the results of this study may suggest that the formation of large colonies of some cyanobacterial species is important to their dominance and/or bloom formation.