The Clara and Garcas lagoons represent lentic environments from the floodplain in the upper Parana River. Thirty six taxa were found, representing four orders (Chroococcales, Oscillatoriales, Nostocales and Stigonematales) and ten families (Synechococcaceae, Chroococcaceae, Merismopediaceae, Nostocaceae, Rivulariaceae, Borziaceae, Pseudanabaenaceae, Phormidiaceae, Oscillatoriaceae and Mastigocladaceae) of cyanobacteria. The most representative family was Pseudanabaenaceae, numbering seven taxa, followed by Oscillatoriaceae and Nostocaceae, both numbering six taxa. Among the 36 taxa, 22 were recorded for the first time in the floodplain of upper Parana River.