Halogens are highly efficient at destroying ozone in the stratosphere, and rising concentrations from human activities has led to depletion of global stratospheric ozone over the last three decades, and formation of the Antarctic “ozone hole”. It is also known that ozone depleting substances (ODSs) enter the stratosphere principally in the tropics, where ascending warm air carries them aloft. The EU-project SHIVA (Stratospheric Ozone: Halogen Impacts in a Varying Atmosphere) aims to reduce uncertainties in the amount of halogen-containing ODSs reaching the stratosphere, and the resulting ozone depletion, in a climate that is changing now, and which will change in the future. During the SHIVA field campaign on board RV Sonne in the South China Sea and Sulu Sea in November 2011, we investigated the potential of phytoplankton being a source for halocarbons emissions in detail by comparing collocated field samples. Phytoplankton parameters such as pigment concentration, functional group type, and PSII efficiency were undergoing a detailed analysis to investigate the relationship between phytoplankton and different halocarbon species. Significant (p < 0.05) relationships were observed between the cyanobacterial marker pigment zeaxanthin, the group of cyanobacteria without Prochlorococcus and methyl iodide (CH3I). In the vertical profiles, high concentration of bromoform was found to correspond to maximum chl a concentration (indicator of total phytoplankton biomass) and maximum 19-hexanoyl-fucoxanthin (the marker pigments for haptophytes) layers observed in depth between 20 to 60 m. These findings are based on statistical analysis based on Kendall’s rank correlations which examine the relationship between halocarbons, phytoplankton groups’ marker pigments and total chl a concentration. Also the relationship of phytoplankton groups and pigments to water temperature, salinity and surface winds only showed for salinity an inverse correlation to total chl-a and especially to cyanobacteria, but a bit weaker also to the other phytoplankton groups.