Cotton (Gossypium L.) fiber is a unique experimental system for studying plant cell elongation and cell wall biogenesis. Arabinogalactan proteins (AGPs) are extracellular proteoglycans and play important roles in various aspects of plant growth and development. In the present work, four AGP genes, GhAGP2, GhAGP3, GhAGP4, and GhFLA1, were cloned from cotton fiber through 5' and 3' rapid amplification of cDNA ends (RACE). All these genes code for classical AGPs containing N-terminal signal sequence, a central domain rich in Ala, Ser, Thr, Pro/Hyp, and C-terminal hydrophobic transmembrane domain. Additionally all the four putative proteins contain two AGP-like domains, one fasciclin-like domain and a putative C-terminal glycosylphosphatidylinositol lipid anchor signal sequence. Northern blotting analysis with gene-specific probes indicates the transcripts of GhAGP2 and GhFLA1 accumulate in Gossypium hirsutum fiber from 5 to 20 days post anthesis, whereas GhAGP3 and GhAGP4 are abundantly expressed during the developmental stage switching from elongation to the secondary cell wall synthesis. Furthermore, quantitative reverse transcription polymerase chain reaction analysis demonstrates that all these fasciclin-like AGP genes are specifically expressed not only in G. hirsutum fibers but also in Gossypium barbadense fibers. The fasciclin-like domains are typically found in adhesion proteins of animal cell, and the specific expression patterns together with presence of fasciclin-like domains suggest roles for fasciclin-like AGPs in cell-to-cell communication during cotton fiber elongation and secondary cell wall development.