Suberin is critical in plant/environment interactions including water and nutrient transport, response to stress and wounding, and pathogen protection. The dominant suberin plant models, potato tuber wound periderm and cork bark have helped elucidate the suberin pathway but suffer from a lack of genetic resources. Wild cotton fibers provide an attractive alternative model. Fibers are among the longest and fastest growing single cells in the plant kingdom, contain a typical dicot cuticle and primary cell wall with a secondary cell wall containing suberin but not lignin. Further, fibers are not essential for seed production, can be grown in vitro, and can be harvested in large quantities. Pigmented fiber is a result of deposition of suberin and waxes in the fiber while the agriculturally-important white cotton fiber is believed to be a result of a null mutation that arose during domestication. Suberin aliphatic content in white fibers is at least 30-fold lower compared to its green counterparts. In this study, we investigated transcriptional differences between fibers of two near isogenic lines of Gossypium hirsutum producing green fiber or white fiber through Illumina RNAseq sequencing. As expected, several genes involved in the suberin biosynthetic pathway were differentially expressed between the green and white fibers. Further analysis of transcriptome data will additionally help identify regulatory elements and relevant mutations, helping tease out biochemical pathway interactions and increasing our understanding of suberin biosynthesis.