A comparison of three analytical methods (the indirect GC‐FPD and MIMS, and direct LC‐MS/MS) for dimethylsulfoniopropionate (DMSP) measurements was conducted to assess their accuracy and reliability. The three methods showed a linear response but are distinguished by their linearity range, the largest being for MIMS. All three methods showed good precision on Alexandrium minutum samples (2–12%). The variability between the three methods when comparing analyses of A. minutum replicates was 11%, with the DMSP measurements by LC‐MS/MS being the highest. This result also confirms that indirect DMSP measurement after hydrolysis for GC or MIMS methods does not lead to an overestimation of DMSP values in A. minutum. A special focus was made on the more recent LC‐MS/MS method including further assays in sample preparation and storage from cultures of the dinoflagellate A. minutum. Dinoflagellate cells should be harvested by gentle filtration (< 5 cm Hg) or slow centrifugation (500 × g) to retrieve the largest DMSP pool. For the LC‐MS/MS method, MeOH used for cell extraction should be added prior to freezing (to prevent DMSP degradation). Samples will then be stable in frozen storage for at least 2 months. Finally, direct and indirect methods are complementary for identifying the exact DMSP fraction among dimethylsulfide‐producing compounds that compose total and particulate DMSP pools issued from newly screened organisms or environmental samples.