Cotton is a commercially valuable fiber crop, renowned for its unique fiber properties. The distinctive features of cotton fiber result from complex interactions among various genetic and molecular pathways. One intriguing aspect of cotton fiber is its natural color, which offers the potential to develop a diverse spectrum of naturally colored cotton fibers. This review aims to elucidate these complexities by examining the inheritance patterns of different fiber colors. Initially, it was proposed that distinct genes were responsible for the color traits of cotton fiber, such as green, brown, and white, based on Mendelian inheritance patterns. Traditionally, a dominant brown fiber gene was believed to be the primary determinant of brown fiber color. However, recent advancements in cotton genetics have identified numerous genes involved in pigment production, regulatory components influencing fiber color, and genetic variants contributing to the diverse range of fiber colors. Key metabolic pathways have been mapped, revealing genes encoding the corresponding enzymes, such as chalcone synthase (GhCHS), which is linked to the flavonoid production pathway and associated with brown and green fiber coloration. Proanthocyanidins and their derivatives, produced via the flavonoid pathway, are the primary pigments in brown fiber. The expression of flavonoid pathway genes is regulated by a major locus Lc1 linked to the MYB transcription factor gene TRANSPARENT TESTA 2 (GhTT2). Brown and green fiber colors are partially dominant traits controlled by single genes, suggesting that gene expression dosage impacts the phenotype of colored cotton. The review highlights the crucial role of genetic and epigenetic processes in determining fiber color. Additionally, it nuanced interaction between dominant brown and white fiber genes and the involvement of multiple loci or modifier genes influencing color intensity.