One unique feature in cyanobacteria and rhodophytes is the presence of pigments-these water-soluble pigments can absorb light in spectral range poorly absorbed by chlorophyll enhancing the spectral range available for cellular conversion to chemical energy. Efficient detection of these compounds is essential for use in physiological studies. A protocol has been designed to extract phycobiliprotein from Leptolyngbya sp. QUCCCM 56, Arthrospira platensis and Rhodomonas sp. combining different disruption methods, extraction solutions, biomass amount and incubation times. In all the strains tested the extraction efficiency proved to match what reported in literature while in regards of the purity all the strain achieved higher values (Arthrospira platensis 100%, Rhodomonas sp. 288% and Leptolyngbya sp. 370%). With the designed protocol it was investigated the effect of light intensity (80–1800 µmol·m-2·s-1) and temperature (20–45°C) on phycocyanin productivity in Leptolyngbya sp. QUCCCM 56. Maximum phycocyanin productivity of 0.091 gPC·d-1·l-1 was measured at 300 µmol·m-2·s-1 and 40°C. The Phycocyanin content decreased at higher light intensities and it increased at higher temperatures. The biomass productivity has one peak at 300 µmol·m-2·s-1, while the temperature increases the productivity at higher values.