In the paper, genetic variation of 52 transgenic insect-resistant cottons was analyzed using SSR and AFLP molecular markers. The results showed among 61 SSR primers 4 could produce polymorphic markers. A total of 102 DNA fragments was scored, among which 25(24.51%) bands were polymorphic. The number of DNA bands per primer ranged from 17 to 30. Nine AFLP primer combinations were selected to perform AFLP fingerprinting from 100. The total bands and polymorphic bands were 618 and 33(accounted for 5.34%), respectively. The number of DNA bands per primer combination ranged from 47 to 81. Mean pairwise genetic distance of 52 varieties (lines) was 4.21, with the range of 2.00 to 5.57. Mean genetic distance for each variety ranged from 3.73 to 4.75. The limited genetic variation was revealed by these results in the population. Based on dendrogram of SSRs and AFLPs, 52 varieties (lines) were divided into three SSR/AFLP-based groups (SAGs). However, SAGs was not accordance with geographic origins of tested varieties (lines).