The aim of the present work was to determine conditions for a reliable analysis of the potentially ichthyotoxic phycotoxin goniodomin A (GDA) by LC-MS/MS. For this purpose, the question under which conditions GDA is chemically stable should be answered. In view of this, stability studies were performed on GDA using organic and aqueous solvents. In addition, similar stability analyses of the congeners GDB/C and analyses with cell extracts of GD producing dinoflagellate species were performed. Different extractants and extraction methods were tested for the gain of GDA from dinoflagellate cells. Selected reaction monitoring (SRM) was used for detection and identification of the compounds accompanying GDA, which was also supported by fragmentation analyses when required. In the course of this work, the analytical system was optimized with respect to the eluent, transitions and adduct ions. The different methods were applied to biological samples from dinoflagellate cell cultures and to field samples from Danish and German coastal waters. The results of the stability analyses showed that GDA is stable in organic solvents but rapidly converts to GDA seco acid in presence of water. To avoid this reaction when extracting natural GDA from cells, it may be useful to process samples directly and to harvest the cells by vacuum filtration. For the analysis of GDs by LC-MS/MS, it is also advisable to use an alkaline eluent, since an acidic eluent favors the interconversion of GDA/B/C and thus distorts the analytical results. With the help of this finding, it was possible to revise the results of a field study among others.