A genetic linkage map of cotton was constructed with a newly developed molecular marker-SRAP (sequence-related amplified polymorphism) using a population consisting of 129 F2 individuals derived from the interspecific cross of Handan208 Pima90. A total of 136 primer pairs were used to detect polymorphisms between the two parents and 76 primer pairs with better polymorphisms were picked out to analyze the F2 population. 285 polymorphic bands were generated in total with an average of 3.75 polymorphic bands per pair of primers. The primer pair showing most polymorphic bands was the combination of me3 and em2, which produced 13 polymorphic bands. The 285 loci were used to construct linkage map with MAPMAKER/EXP3.0 and 237 loci were mapped at a LOD≥3.0 on 39 linkage groups. The total length of the map is 3030.7 cM, covering 65.4% of the whole cotton genome, and the average distance between adjacent markers is 12.79 cM. All the markers are distributed evenly among the linkage groups without clustering of loci. This is the first linkage map of cotton comprised of SRAP markers. A genetic linkage map of cotton was constructed with a newly developed molecular marker-SRAP (sequence-related amplified polymorphism) using a population consisting of 129 F2 individuals derived from the interspecific cross of Handan 208 Pima 90. A total of 136 primer pairs were used to detect polymorphisms between the two parents and 76 primer pairs with the better polymorphisms were picked out to analyze the F2 population. 285 polymorphic bands were generated in total with an average of 3.75 polymorphic bands per pair of primers. The primer pair showing most polymorphic bands was the combination of me3 and em2, which produced 13 polymorphic bands. The 285 loci were used to construct linkage maps with MAPMAKER / EXP3.0 and 237 loci were mapped at a LOD> 3.0 on 39 linkage groups. The total length of the map was 3030.7 cM , covering 65.4% of the whole cotton genome, and the average distance between adjacent markers is 12.79 cM. All the markers are distributedially among the linkage groups with out clustering of loci. This is the first linkage map of cotton comprised of SRAP markers.