Gl e 2 is a mutant gene that controls glandless trait in cotton plants and seeds. It is an important gene resource to gossypol-free cottonseed breeding. The objective of this research was to develop SSR markers tightly linked with Gl e 2 by using the F 2 segregating population containing 1599 plants derived from the cross of G. hirsutum genetic standard line TM-1 and G. barbadense glandless mutant line Hai-1. Genetic analysis suggested that the Gl e 2 was an incomplete dominant gene. Based on the backbone of genetic linkage map from G. hirsutum × G. barbadense BC 1 published by our laboratory, Gl e 2 was located between CIR362 and NAU2251b, NAU3860b, STV033, with a genetic distance 9.27 and 0.96 cM, respectively. This result is useful for cloning Gl e 2 gene by map-based cloning method.