Microbial flocculation is investigated as a separation technique for harvesting marine microalgae for the production of biodiesel. Organic carbon (acetate, glucose or glycerine) was used as substrate for the growth of flocculating microbes in situ. Under stress, due to nutrient depletion, these microbes produced extracellular polymeric substances that promote flocculation of the coccolithophorid alga, Pleurochrysis carterae. Maximum recovery efficiency was achieved at low concentration of organic substrate (0.1 g L −1 ) and with a long mixing time (24 h); an average recovery efficiency of over 90% and a concentration factor of 226 were achieved. The recovery efficiency is positively correlated with mixing time (R 2 =0.90). The concentration factor is negatively correlated to the product of substrate concentration and mixing time (R 2 =0.73). The microalgae cells were not under stress and remained viable, thus potentially allowing media to be reused in large-scale processes without further treatment. Other advantages of the process are that no metallic flocculants were required and the organic substrates are readily available, e.g. glycerine is a byproduct of biodiesel production and acetic acid may be produced by anaerobic digestion of the biomass residue after lipid extraction. Further research is required to optimise the process.