Different clinical types of algae-related poisoning have attracted scientific and commercial attention: paralytic shellfish poisoning (PSP), diarrhetic shellfish poisoning (DSP), and amnesic shellfish poisoning (ASP). Bioassays are common methods for the determination of marine biotoxins. However, biological tests are not completely satisfactory, mainly due to the low sensitivity and the absence of specialized variations. Therefore, many efforts have been made to determine algal toxins using different chemical methods. In this context LC-MS methods replaced HPLC methods with optical detectors, allowing both effective seafood control and monitoring of phytoplankton in terms of the different groups of marine biotoxins. This chapter describes state-of-the-art LC-MS/MS methods for the detection and quantitation of different classes of phycotoxins in shellfish matrices. These classes include the highly hydrophilic paralytic shellfish poisoning (PSP) toxins. , which have been traditionally separated by ion pair chromatography followed by derivatization and fluorescence detection. However, the ion pair reagents added to the mobile phases are not compatible with mass spectrometry, so a new chromatographic system had to be developed. Hydrophilic interaction liquid chromatography (HILIC) has been shown to be useful in the separation of PSP toxins and is described in detail within this chapter. Another important class of phycotoxins are diarrhetic shellfish poising (DSP) toxins. This group traditionally comprises okadaic acid and dinophysistoxins (DTXs), pectenotoxins (PTXs) and yessotoxins (YTXs). The latter two groups are often associated with diarrhoea causing DTXs, but recently turned out not to have diarrhetic effects by themselves, which means in the strict sense they are no DSP toxins. For this reason the term “lipophilic” toxins rather than DSP is increasingly applied to for this group of toxins. The most recently described shellfish poisoning syndrome, azaspiracid shellfish poising (AZP) is caused by azaspiracids, which in turn are diarrhetic, but usually are treated separately as AZP. The last group of regulated shellfish toxins is the amnesic shellfish poisoning (ASP) toxin domoic acid, produced by species of the genus Pseudo-nitzschia.