Phycobiliproteins (PBP) are naturally occurring water-soluble fluorescent pigments produced by cyanobacteria, eukaryotic algae, and cryptomonads. These serve as accessory pigments for photosynthetic light harvesting complex. PBP are organized in supramolecular complex structures called as phycobilisomes which are assembled in a regular array on the outer surface of thylakoid membrane and lie adjacent to photosynthetic reaction center of PS-II in cyanobacteria and red algae. Depending upon the absorption maxima, these pigments are classified as phycoerythrin (λmax 540–570 nm), phycocyanin (λmax 590–630 nm), and allophycocyanin (λmax 620–655 nm). Being non-toxic and non-carcinogenic in nature, these can be safely used as coloring agents in food and cosmetics. These pigments have also been reported to exhibit a variety of pharmacological properties such as antioxidant, anti-inflammatory, neuroprotective, and hepatoprotective effect. Cyanobacterial species such as Anabaena sp., Gloeotrichia natans, Nostoc sp., Spirulina platensis, Spirulina fusiformis have been reported to produce PBP in significant amounts. Out of these, Spirulina platensis has been employed for commercial production of PBP. Since cyanobacteria are cosmopolitan in nature and grow in varied and extreme habitats such as hot water springs, cold deserts, acidic and alkaline conditions, thus, methods for extraction and purification of PBP produced by different cyanobacteria and red algae growing in various habitats have been presented in this chapter.