The simultaneous detection of cyanotoxins is an important issue in order to prevent intoxications. In the present paper an Ultra Performance liquid Chromatography tandem mass spectrometry UPLC-MS/MS method was developed in order to simultaneously identify and quantify cylindrospermopsin (CYN), several microcystins (MC-LR, MC-RR, MC-YR) and some anatoxin-a (ATX-a) analogues. By using this new method all these toxins can be quickly separate. In addition the amino acid phenylalanine (Phe) can also be separate and therefore misidentifications with ATX-a can be avoided. By using this new method the presence of these toxins was studied in samples collected in several German localizations within the sampling program of the European Project μAqua (Universal microarrays for the evaluation of fresh-water quality based on detection of pathogens and their toxins). In these conditions, several ATX-a analogues, Phe, MC-LR and MC-RR were reported in samples collected.