The use of foam fractionation followed by aqueous two-phase extraction has emerged as a potential alternative to traditional liquid chromatography, hitherto irreplaceable in the purification of phycobiliproteins. The crude extracts of C-phycocyanin and allophycocyanin were obtained after Thermosynechococcus PCC 6715 biomass disintegration. The FF process with air flow of 2.4 L·h ^-1 resulted in purification factors up to 1.47 and partitioning coefficients of about 39, and did not require the addition of surfactants. A temperature of 35˚C allowed for the highest partitioning coefficient of 67.6 and yield of 76%; however, the purity of C-PC in condensate at this temperature was lower than at 25˚C. ATPE was tested in 20 different systems consisting of polyethylene glycol and phosphate or citrate salts, of which PEG1500-citrate gave the highest purification factor value of 2.31. Conversely, a partitioning coefficient of 2416 and 1094 were obtained for the PEG1500-phosphate and PEG3000-phosphate systems, respectively. Interestingly, the use of FF condensate in subsequent ATPE step resulted, for the first time, in the separation of the polymer phase into two fractions, one contained C-phycocyanin and the other allophycocyanin. It can be concluded that the use of a two-step system of FF and ATPE is a viable way to separate phycobiliproteins.