Fusarium wilt is one of the most important diseases of Gossypium hirsutum
L. and causes heavy damage in all cotton growing areas of China. Resistance to the disease is controlled by one dominant gene in upland cotton. It is easy to transfer the resistance gene into susceptible cultivars, but whether the resistance gene has deleterious effects on cotton agronomic traits is unknown. In this experiment, five pairs of resistant- susceptible near isolines were used to evaluate the genetic effects of cotton Fusarium resistance genes on agronomic traits in heavily infested and non-infected fields, Three genotypes with gene Fw2 or fw2 under J1 or E18 background derived from a backcross introgression program. The other 2 pairs, J1R/J1S, and E18R/E18S were selected in the heavily infested fields for resistance or susceptibility. The resistance identification of 5 pairs of near-isolines indicated the two methods of developing resistant-susceptible near-isolines were effective. Susceptible lines yield less because of fewer and smaller bolls, lower lint percentage and low density. Generally there were no significant differences between each pair of the near-isolines, except that one pair differed significantly in seed index and fiber length. The results indicated that the resistance gene Fw2 has no deleterious impact on agronomic traits (including plant height, number of fruit branches, boll size, seed index, lint index, and lint percentage) and fiber quality (including fiber length, strength, elongation and fineness). It should be determined if the resistance gene in J1R affects 2.5% fiber span length.