Photosynthesis has existed on the earth for about 4 billion years, and the photosynthetic organisms have emerged with the production of photosynthesis. In order to effectively capture light energy and adapt their living environment, algae and higher plants have evolved different light-harvesting antenna systems during the long evolution, one is the chlorophyll based light harvesting systems present mainly in terrestrial organisms, such as higher plants; and the other is the phycobiliprotein (PBP) based phycobilisome system mainly in aquatic organisms, such as cyanobacteria, red algae and cryptophytes. As a special light-harvesting pigment-protein complex, PBP can not only capture light energy, also shows many unique characteristics, such as good fluorescent properties and lots of pharmaceutical activities. Therefore, PBPs have been extensively studied and commercially used in foods, cosmetics, biotechnology detection, pharmacological and medicine fields. Due to its broad excitation spectrum, nontoxic, stable fluorescence and high quantum yield, PBPs have also employed as valuable fluorescent probes for immunological diagnosis. At present, there are mainly two ways to obtain fluorescent PBPs, one is to purify PBP directly from natural algae, and the other is to express recombinant PBP using genetic engineered host cells. Purification of PBPs from natural algae has many disadvantages, such as higher cost, complicated processes, and many by-products. Using genetically engineered cell biotechnology, large-scale and low-cost production of recombinant PBPs can be achieved, which can help solve problems such as source, quality control and so on. Since natural PBPs are mostly in the form of polymers such as trimers or hexamers, it is difficult to study the assembly process. Through genetic engineering techniques, monomers or subunits can be obtained, which will help to study the assembly process of PBP. In addition, novel recombinant PBPs can be produced by molecular design to improve their fluorescence and biological activity. The study of the biosynthesis will help to elucidate the relationship between the structure and spectral properties of PBPs and provide a basis for the construction of solar energy utilization systems. This review mainly focuses on the progress of combinational biosynthesis and in vivo reorganization of PBP in heterologous genetically engineered host cells, with emphasis on different genes coding for apo-PBPs and genes coding for different enzymes which catalyze the production of phycobilins from endogenous heme, along with the recent progress of three types of lyases which catalyze the covalently binding of phycobilins with apo-PBPs. The possible applications of these valuable recombinant PBPs were proposed as well.