Oranges, lemons, and mandarins are among the most popular fruits consumed worldwide; they are valued for their flavor, color, and texture. Numerous intricate genetic, biochemical, and physiological mechanisms affect the quality of citrus fruits, especially during ripening. Enhancing the quality, shelf life, and marketability of fruit requires an understanding of the genetic foundations underpinning important ripening characteristics such as texture, flavor, and color. The purpose of this research was to identify and describe the genes that control citrus ripening, with an emphasis on the genetic regulation of the fruit's texture, flavoring, and color development. We examined the gene expression profiles at different phases of fruit ripening in a variety of citrus cultivars, such as sweet oranges and mandarins, using a mix of transcriptomic and genomics techniques. Differentially expressed genes (DEGs) that are involved in fruit development were identified using RNA sequencing, and these genes were linked to important phenotypic features using genome-wide association studies (GWASs). The fruit texture was discovered to be significantly influenced by genes that encode enzymes that are involved in the manufacture and degradation of cell wall components, such as pectin methylesterases and polygalacturonases. Genes that produce flavor and fragrance molecules, such as terpene synthases, and enzymes that are involved in the phenylpropanoid pathway were also investigated. Another important area of study is the control of fruit's color, which is mostly caused by carotenoid production. An in-depth analysis was carried out on genes such as phytoene synthase (PSY) and lycopene β-cyclase (LCYB), which control the build-up of carotenoids and, consequently, the orange hue of mature citrus fruit. We also examined how ethylene, a hormone that is important for fruit ripening, interacts with these genes and how it regulates their expression. Our goal was to achieve a thorough understanding of the molecular mechanisms influencing citrus ripening features by describing these genes. Ultimately, breeding programs can use the identification of genetic markers that are linked to desired fruit attributes such as texture, flavor, and color to create new citrus varieties that are more palatable to consumers, have longer shelf lives, and are more resilient to environmental stressors. This study contributes to the future of sustainable agriculture in the citrus sector by opening the door for the use of molecular breeding techniques in citrus development.