By using AFLP technique polymorphism analysis was performed between a fuzzlesslintless mutant line and its isogenic wild-type line, Xuzhou 142. Out of 6,360 bands produced by 64 pairs primers, a fragment, named as CF1, appearing stably in wild-type line, Xuzhou 142. This polymorphism was further verified using several normal fiber varieties and F2, F3 populations from the cross of fuzzless-lintless mutant line with a high-lint-percentage variety Yumian No. 1. The cosegregation of CF1 and fibrogenesis was proved, which suggested that CF1 can be used as a molecular marker for cotton fibrogenesis. The CF1 segment was cloned into PUCm-T Vector and then sequenced. The putative amino acid sequences, is an analogue to phenol hydroxylase alpha subunit, outer surface protein C, NADH dehydrogenase subunit 1, NADH-ubiquinone oxidoreductase, 2-oxoacid ferredoxin oxidoreduct and hypothetical 14.5kD protein.