Chlorella is a strong candidate as a potential production organism for future biofuels and other algal-derived products, but contamination by grazing protozoa is a major constraint to its commercial production on a large scale. In this study, a mixotrophic flagellate chrysophyte that targeted Chlorella in mass culture was observed in samples from outdoor massive photobioreactor systems. Data from field studies demonstrated that once the predatory flagellate was observed in the algal culture, there was a dramatic reduction in Chlorella cell concentration. The grazer was identified as Poterioochromonas malhamensis, based on both morphology and molecular barcoding employing 18S rDNA gene sequences. Transmission electron microscopy revealed that P. malhamensis digested the ingested Chlorella sorokiniana cells within a food vacuole, with residual cell wall from the prey being observed in the final phase. It was noted that during the process of ingesting and digesting the C. sorokiniana cells, the chloroplast of P. malhamensis reduced in size, whereas the number and volume of mitochondria increased. After the prey had been completely digested, the chloroplast and mitochondria of P. malhamensis returned to their pre-feeding status. Feeding experiments in the laboratory demonstrated that cell concentrations of C. sorokiniana and P. malhamensis were negatively correlated. Furthermore, once P. malhamensis reached 5 x 10(5) cells mL(-1) and the ratio of C. sorokiniana to P. malhamensis was in the range 15: 1 to 30: 1, the cell concentration of the C. sorokiniana culture decreased dramatically. The optimal temperature for P. malhamensis grazing on C. sorokiniana was 25 degrees C; the grazing ability of P. malhamensis in light conditions was higher than that in dark conditions; and P. malhamensis preferred weakly acidic conditions. In addition, it was demonstrated that this flagellate could graze on other common microalgae of commercial value. On the basis of its capacity to ingest a wide spectrum of phytoplankton, and its wide environmental range and global distribution, this contaminant has the potential to be a common problem in microalgal mass cultures and warrants further study.