The escalating interest in utilizing phycobiliproteins (PBS) across industrial, biotechnological, pharmaceutical and clinical domains necessitates the establishment of robust and reliable analytical protocols for their comprehensive and precise analysis. The vibrant coloration and strong fluorescence of phycobiliproteins are attributed to multiple tetra-pyrrole prosthetic groups known as bilin chromophores. Consequently, they exhibit high absorption coefficient (105 to 106) and high fluorescent quantum yield (0.51 to 0.98), which make them ideal for their analysis based on spectral characteristics. Recent advances in analytical protocols for phycobiliprotein analysis emphasized the importance of high-resolution techniques such as HPLC and LC–MS for the precise identification and characterization. Although developing techniques that minimize the protein degradation is crucial for the accurate analysis of phycobiliproteins, preserving the native state of the molecules remains essential. The accurate quantification of phycobiliproteins in complex mixtures is challenging due to the potential interferences from different other proteins and required advanced analytical techniques like proteomic approaches along with the use of bioinformatics tools, which allows thorough interpretation and analysis. Combining the computational and spectrometric techniques together will offer a deeper insight highlighting the necessity of multidisciplinary approaches. In summary, this chapter briefly examines recent advancements in the analytical protocols in the analysis of phycobiliproteins such as different spectroscopic, chromatographic techniques along with other contemporary techniques for phycobiliprotein analysis. It highlights the key lessons learned and also outlines the future challenges and opportunities in advancing our understanding and utilization of these pigments in diverse fields.