Cyanotoxin standards are commercially available from various suppliers. To investigate the potential impact of different sources on the comparability of cyanotoxin monitoring results among different methods and studies, this study evaluated the quality of 86 cyanotoxin standards from nine vendors via enzyme‐linked immunosorbent assay and liquid chromatography–tandem mass spectrometry. Substantial variabilities between vendors (up to 60%) and between lots (up to 98%) were observed for most of the standards. In addition, some of the microcystin standards had up to 11% of other microcystins as impurities. Compared to non‐certified analytical standards, certified standards showed much better agreement, with standards variations below 15% for all tested toxins. This study highlights the importance of developing and applying unified and certified standards for cyanotoxin analysis to improve the consistency and comparability of results. If different sources/lots of standards are used, they need to be cross‐checked to evaluate the potential impacts on results.