This study presents results of the inventory of algal flora conducted between August 2007 and May 2008 in 18 lakes of the middle Rio Doce lake system, most of which is in the state of Minas Gerais, Brazil. We recorded 481 taxa, increasing the known total phytoplankton diversity of the region (gamma diversity) by 80%. The following classes were represented: Zygnematophyceae (171 taxa), Cyanobacteria (101), Chlorophyceae (71), Bacillariophyceae (42), Euglenophyceae (43), Trebouxiophyceae (24), Dinophyceae (8), Xanthophyceae (8), Chrysophyceae (6), Cryptophyceae (6) and Oedogoniophyceae (1). We identified 221 taxa that were rare (restricted to one or two lakes), and 101 that were considered representative (present in at least nine lakes). Botryococcus braunii, Elakatothrix genevensis, Planktolyngbya limnetica, Peridinium pusillum, Trachelomonas volvocina, Cosmarium contractum, Staurastrum forficulatum, Staurastrum leptocladum, Staurastrum rotula, and Staurodesmus dejectus were present in all lakes. Richness varied from 95 taxa (in Lake Gambazinho) to 168 taxa (in Lake Palmeirinha). Jaccard indices were low, and the highest similarities between lakes were 53% (Ferrugem/Ferruginha), 47% (Central/Almécega) and 46% (Águas Claras/Palmeirinha), demonstrating high environmental and biotic dissimilarities between lakes. Geographic distance was not significantly associated with floristic similarity, suggesting that local factors are more important than are regional ones in shaping the phytoplankton composition of lakes.