A photosynthetic bacteria pond system was applied to the treatment of food industrial wastewater and recovery of carbon in the form of purple non-sulphur bacterial (PnSB) cell. The effect of infra-red transmitting filter on the selection of microbial groups in the system was investigated. It was found that more than 90% of organic removal could be achieved when the system was operated at HRT of 3 to 10 days, even though some fluctuations were observed at lower HRT. Infra-red transmitting filter could suppress the growth of microalgae in the system and allow the purple non-sulphur to grow in the system. Nevertheless, they could be outgrown by sulphate-reducing bacteria at higher organic loading rates. The growth of purple sulphur bacteria associated with sulphate reducing bacteria was also observed. ORP is a crucial operating factor to control the system under micro-anaerobic conditions which is preferred to the growth of purple non-sulphur bacteria.