Trichomes are hair cells derived from specialized epidermal cells on the surfaces of land plants. These hairs are produced as a result of the outward growth of one or more epidermal cells and have diverse structures and functions. Some types of the trichomes have significant economic value, such as the trichomes of cotton seeds, called cotton fibers, the most important natural fiber in the textile industry. In this study, trichome genes from the model plant species, Arabidopsis were used to mine homologous trichome gene or EST sequences in cotton. Single nucleotide polymorphisms (SNPs) were identified by constructing contigs for the tetraploid cotton in comparison with their diploid progenitors. The putative SNPs provide a basis for quantitative trait locus (QTL) mapping and candidate gene analysis.