he phycobiliproteins (PBPs) are antenna pigments composed of apoprotein covalently bound to phycobilin (tetrapyrrole-chain chromophores). The main PBPs are phycoerythrin (PE), phycocyanin (PC), and allophycocyanin (APC) that absorb at 550, 620, and 650 nm, respectively, and are associated with phycobilisomes in cyanobacteria and rhodophytes. At present, it is of industrial-biotechnological interest to use natural dyes, mainly blue pigments with food-grade quality. The main known source is PC although unstable for use in industrial food processes because it degrades at temperatures above 45°C and it is sensible to light and pH. Recently, it was reported that some extremophile microorganisms, such as the thermophilic red algae Cyanidioschyzon merolae, are able to produce PC which is stable at pH 5 at 83°C, but with a half-life of 40 min. Another interesting example is a halophilic cyanobacteria Euhalothece sp. that can grow at 45°C, pH 6–9, and 12% NaCl, which allows low risk of microbial contamination. The PC from this cyanobacteria was purified up to analytical grade (purity >2) and was stable at 45°C, pH 5–8. These strains open the possibility to explore more biotechnological conditions that would allow to generate a pigment with a longer half-life for industrial use. The previous studies about PBPs have been focused on the way to prevent the loss of color due to PC degradation. In this regard, several preservative substances were tested such as citric acid, fructose, beet pectin, and crosslinking with methylglyoxal (MGO). Formulation in anionic micelles was also investigated. The PC from Spirulina platensis improved its stability in the presence of citric acid (4 mg/mL) at 35°C for 15 days. A correlation has been shown between sugars (mainly fructose) and PC stability, but the use is limited for pastry and confectionery due to the high sugar content. On the other hand, sodium dodecyl sulfate (SDS) micelles stabilize the nonprotonated (blue) forms of PC and prevent the formation of protonated forms (green) at low pH. The challenge in the field of PBPs is to improve the stability at high temperatures for its use in food in order to guarantee food safety and overall quality. This can be achieved by using genetics, molecular tools, and biotechnological approaches including extremophile microorganisms.