Phytoplanktonic biodiversity is important for both basic and applied ecological studies. We compared taxonomic identification and quantification trhough sequencing with those from microscopy studies for a total of 300 freshwater samples collected during a time period of 20 years. The data showed that the two methods have different best resolution levels, with microscopy being better at identifying species, while sequencing was better at identifying genus, suggesting the methods should be used in conjunction.