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Marine phytoplankton play critical roles in the biogeochemistry of open and coastal oceans. However, the impact that individual species have on an ecosystem-wide scale can strongly depend on the production of cellular compounds, especially those that are climatically active such as dimethylsulfide (DMS). Herein, we use sorting flow cytometry to separate a distinct phytoplankton population from four samples taken along the Patagonian shelf near the Falkland Islands. Morphological, genetic, and biochemical analyses demonstrated that three of the sorted samples were dominated by a bloom of the dinoflagellate Prorocentrum minimum. Cellular quotas of the DMS-precursor dimethylsulfoniopropionate (DMSP) ranged from 1.23–4.11 pg cell−1 in the same population at different sampling stations. Causes of this variability may be due to different growth stages of the P. minimum bloom or changes in other environmental variables. Overall, in situ intracellular DMSP concentrations were lower than what would be expected based on previous, culture-based measurements. We demonstrate the difficulties inherent in sorting individual phytoplankton species from natural samples in order to determine in situ species-specific cellular quotas of important biogeochemical compounds.