Abstract: The genetic diversity of colored cotton was studied by SRAP, and the results of SRAP-PCR of 30 spices of cotton materials were analyzed by NTSYS software. Twenty-nine primer combinations were selected from 88 primer pairs , which amplified 132 polymorphic bands with an average of 4.55 polymorphic bands per primer pair. Cluster analysis by using UPGMA method based on the data of SRAP amplified bands by 29 primer pairs showed that Jaccard’s similarity coefficient ranged from 0.5405 to 0.9109. The results indicated that the genetic difference between colored cotton and white cotton can be distinguished by SRAP, and SRAP molecular marker can be applied to study the colored cotton genetic diversity efficiently.