Cotton fibers, important natural raw materials for the textile industry, are trichomes elongated from epidermal cells of cotton ovules. To date, a number of genes have been shown to be critical for fiber development. In this study, the roles of genes encoding fasciclin-like arabinoglactan proteins (FLAs) in cotton fiber were examined by transforming RNA interfering (RNAi) construct. The RNAi according to the sequence of GhAGP4 caused a significant reduction of its mRNA level, and the expression of other three FLAs (GhAGP2, GhAGP3, GhFLA1) were also partially suppressed. The fiber initiation and fiber elongation were inhibited in the transgenic plants. As for the mature fibers of transgenic cotton, the fiber length became significantly shorter and the fiber quality became worse. In addition, the RNAi of GhAGP4 also affected the cytoskeleton network and the cellulose deposition of fiber cells. Through ovule culture, it was found that the expression of cotton FLA genes were upregulated by GA(3), especially for GhAGP2 and GhAGP4. These results indicate that the FLAs are essential for the initiation and elongation of cotton fiber development.