Abstract: 【Objective】 To provide reference for the utilization of Fusarium wilt resistant cotton breeding materials and marker-assisted selection by carrying out SSR (Simple Sequence Repeat) molecular marker association analysis on 204 island cotton germplasm resources. 【Method】 40 pairs of SSR markers were designed based on the disease resistance gene sequences studied in the previous laboratory.The specificity of marker primers was screened by polyacrylamide gel electrophoresis, and 204 samples of island cotton germplasm resources were identified. 【Results】 (1) Six pairs of primers were selected from 40 pairs of primers with polymorphism, and two molecular markers, CHS-04 and CHS-05, were selected after repeated repeats, both from the flavonoid metabolic pathway; (2) Molecular markers and laboratory identification of 204 germplasm were used to identify Fusarium wilt.The results of comprehensive analysis showed that the primers CHS-04 amplified bands had a consistent rate of 41.67%-52.94% with an average of 46.67%.The coincidence rate of the amplified band of CHS-05 primer and the population material ranged from 30.39% to 54.68% with an average of 35.78%. 【Conclusion】 Primers CHS-04 and CHS-05 can be used as molecular markers for identification of Fusarium wilt resistance of Sea Island Cotton.