Four variant lines, HB1, HB2, HB3 and HB4, were derived from progenies of upland cotton (Gossypium hirsutum) cultivar Yumian 17 that had been transformed with genomic DNA from sea island cotton, Gossypium barbadense, using the pollen tube pathway (PTP) method. They showed significant differences from the wild-type recipient in terms of fibre quality, lint percentage, boll weight and other agronomic traits. The four variant lines also differed from the wild-type recipient in the amplification products of two SSR loci, indicating that the DNA of G. barbadense had been introduced into the genome of the recipient and was inherited stably. On the other hand, the agronomic traits of another three lines (HB5, HB6 and HB7) derived from the same transformation experiment were identical to those of the wild-type recipient, indicating that G. barbadense DNA had not integrated into the genome of these lines. A combination of the analyses on agronomic traits and SSR markers indicated that transgenic upland cotton strains produced by the PTP method could become homozygous in only a few generations and the foreign DNA introduced during the transformation experiments could be inherited stably in the transgenic progenies.