Carotenoids are the principal pigments in the loquat. Although the metabolic pathway of plant carotenoids has been extensively investigated, few studies have been explored the regulatory mechanisms of loquat carotenoids because knowledge of the loquat genome is incomplete. The chromoplast-specific lycopene β-cyclase gene (CYC-B) could catalyze cyclization of lycopene to β-carotene. In this study, the differential accumulation patterns of loquat with different colors were analyzed and virus-induced gene silencing (VIGS) was utilized in order to verify CYC-B gene function. Using a cloning strategy of homologous genes, a CYC-B gene orthologue was successfully identified from the loquat. At a later stage of maturation, CYC-B gene expression and carotenoids concentrations in the 'Dawuxing' variety were higher than in 'Chuannong 1-5-9 , possibly leading to the difference in pulp coloration of loquat. Interference of CYC-B gene expression in the loquat demonstrated clear visual changes. The green color in negative control fruits became yellow, while TRV2-CYC-B silenced fruits remained green. CYC-B gene expression and total carotenoid content in the pulp decreased by 32.5% and 44.1%, respectively. Furthermore, multiple key genes in the carotenoid metabolic pathway synergistically responded to downregulation of CYC-B gene expression. In summary, we provide direct evidences that CYC-B gene is involved in carotenoid accumulation and coloration in the loquat.They participate in the assembly of photosystems and perform a significant role in light capture, whereby they absorb light in a range of the blue spectrum broader than that achieved in chlorophyll. The excited carotenoids undergo excitation energy transfer to chlorophyll [8,9]. Carotenoids protect the photosynthetic apparatus from photooxidative damage caused by excess light energy through the quenching of both singlet and triplet state chlorophylls [9,10]. Carotenoids are conducive to produce scents and flavors that attract insects and animals for pollination and seed dispersal [11]. They are also significant precursors for the biosynthesis of metabolites, such as vitamin A, strigolactone, and abscisic acid [12][13][14][15][16]. Furthermore, carotenoids are thought to protect the human body from oxidative stress by removing free radicals, which can prevent cancer, cardiovascular diseases, and other chronic diseases [17][18][19].Sites for the biosynthesis and accumulation of plant carotenoids are plastids, containing chloroplasts and chromoplasts [20]. The plant carotenoid biosynthesis and cleavage pathway is shown in Supplementary Figure S1. Geranylgeranyl diphosphate (GGPP), a precursor of carotenoid metabolism, is catalyzed to produce phytoene by phytoene synthase (PSY). Phytoene is the first carotenoid molecule and undergoes desaturation and isomerization to form lycopene. This process is catalyzed by desaturases (phytoene desaturase, PDS; ζ-carotene desaturase, ZDS) and isomerases (carotene isomerase, CRTISO; 15-cis-ζ-carotene isomerase, ZISO). Cyclization of lycop...