Genome-wide association study is an approach for identifying the genes that underlie common diseases and related quantitative traits. This strategy combines a comprehensive and unbiased survey of the genome with the power to detect common alleles with modest phenotypic effects. In cottonMD, we collected 23 traits of 4180 cotton accessions, including Angle between fruit branches (AFB), Boll abscission rate1 (AR1), Boll opening day (BD), Boll weight (BW), Fiber elongation rate (FE), Fiber length (FL), Fiber strength (FS), Fiber uniformity (FU), Fiber upper half mean length (FUHML), Flowering day (FD), Height of the node of the first fruiting branch (HFFBN), Hundred-grain weight (WH), Leaf pubescence amount (LPA), Lint index (LI), Lint percentage (LP), Lint weight (LW), Micronaire value (MV), Number of fruit branches (BFN), Plant height (PH), Seed cotton weight (SW), Seed index (SI), Short fiber rate (FR), Yelid and performed GWAS combining their genotypes using GEMMA. The most significant SNP in every 500kb-window was retained. User can browse GWAS results and search significant SNPs and genes of 6 fiber-associated traits.