The growth and nutrient removal capacity of the cyanobacterium Phormidium bohneri and of the endogenous microalga Micractinium pusillum were investigated for the biotreatment of a cheese factory anaerobic effluent. Phormidium bohneri demonstrated higher growth rate (k = 0.62 d(-1)) and biomass yield (329 mg dry mass l(-1)) than that of M. pusillum (0.35 d(-1) and 137 mg dry mass l(-1)) over four days. In the presence of this cyanobacterium or this microalga, ammonia was completely removed after four days, although the kinetics of removal were different for both species. Rates of removal of phosphorus in the presence of P. bohneri and M. pusillum were 2.9 and 2.5 mg P-PO43-.l(-1).d(-1), respectively. These results were interpreted as a function of different factors, such as the increase in pH and aeration time.