Two different assays have been developed and used in order to investigate the optimal conditions for derivatization and detection of acid β-N-methyl-amino-l-alanine (BMAA) in a cyanobacterial sample. BMAA was extracted from cyanobacterial cultures both from the cytosolic (“free”) fraction and in the precipitated (“protein”) fraction using a newly developed extraction scheme and the sample matrix was standardized according to protein concentration to ensure the highest possible derivative yield. A rapid and sensitive HPLC method for fluorescence detection of the non-protein amino acid BMAA in cyanobacteria, utilizing the Waters AccQ-Tag® chemistry and Chromolith® Performance RP-18e columns was developed. Using this new method and utilizing a different buffer system and column than that recommended by Waters, we decreased the time between injections by 75%. The limit of quantification was determined to be 12 nmol and limit of detection as 120 fmol. The linear range was in the range of 8.5 nmol–84 pmol. Accuracy and precision were well within FDA guidelines for bioanalysis.