Anaerobic treatment of pig and dairy manure was studied in the laboratory with 2-stage anaerobic sequencing batch reactor (ASBR) systems. The effects of anaerobic treatment on odour control in subsequent storage units were evaluated. The results show that the ASBR systems worked well for both dairy and pig manure at an hydraulic retention time (HRT) of 6 days and volatile solid (VS) loading rates of 1, 2, 3, and 4 g/litre/day. VS reductions from 26.1 to 47.5% were achieved for dairy manure while much higher VS reductions (54.7-86%) were achieved for pig manure. The thermophilic-mesophilic ASBR system had better performance in treating dairy and pig manure with 6-15% more VS removals than the mesophilic-mesophilic ASBR system. Odour test results showed that the anaerobic treatment effectively reduced offensive odour generation during storage. Untreated dairy and pig manure exhibited strong offensive odour with very high H2S and mercaptan concentrations in the headspaces of storage jars. The anaerobically treated manure, however, showed minimal residual odours while in many cases, H2S and mercaptans were not detectable. This study showed that the newly developed temperature-phased ASBR has great potential for application in animal waste treatment for organic removal, energy production, and effective odour control.