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Naturally colored cotton fiber is environment-friendly but has monotonous color and poor fiber quality. Identification of green fiber or fuzz genes would aid in investigating the biosynthesis of green pigments in cotton fibers. In this study, we established a mapping population and found that the Lgf trait (white lint and green fuzz) from Gossypium hirsutum race latifolium is controlled by an incompletely dominant gene. The Lgf locus was mapped to a 71-kb interval on chromosome 21 containing seven genes, including a transcription factor with similarity to Arabidopsis MYB9. Harboring 13 SNPs and a 4-bp insertion/deletion in its promoter, GhMYB9 was highly up-regulated in the critical period for green pigment development in fuzz. Virus-induced gene silencing of GhMYB9 in a green-fuzz accession of G. hirsutum race latifolium TX-41 conferred white or light green fuzz. These results suggest that GhMYB9 is an important contributor to green pigments in cotton fiber and shed light on the regulatory mechanism controlling green pigmentation.