Microalgae culture has been raised due to high biotechnological potential associate a production and identification of several metabolites with interest, such as natural pigments with unique structural features. In this sense, the aim of this work was to evaluate the chlorophyll production from Phormidium autumnale using wastewater from poultry and swine slaughterhouses as culture medium. The microalgae cultivation was conducted in a bubble column bioreactor, operating in batch system. The experimental conditions were established as, initial inoculum concentration of 100 mg.L-1 (dry weight), pH of 7.6, temperature of 26 ºC at constant aeration of 1 volume of air per volume of medium per minute, in absence of light. The chlorophyll fraction was extracted exhaustively, using ethyl acetate and methanol. The quantitative analysis was performed by spectrophotometer with diode array and the identification in HPLC-PDA by the comparison with the standard retention time. The results indicate that in the microalgal biomass was found an amounted of 813.54µg/g and 198.75µg/g of chlorophyll a and chlorophyll b respectively. In fact according with these results, the microalgae Phormidium autumnale show a potential as renewable source for the obtainment of natural pigments.