Fructose-1,6-biphosphate aldolase (FBA) is a multifunctional enzyme in plants, which participates in the process of Calvin-Benson cycle, glycolysis and gluconeogenesis. Despite the importance of genes in regulating plant growth, development and abiotic stress responses, little is known about their roles in cotton. In the present study, we performed a genome-wide identification and characterization of in . Totally seventeen genes were identified. According to the analysis of functional domain, phylogenetic relationship, and gene structure, genes were classified into two subgroups. Furthermore, nine were predicted to be in chloroplast and eight were located in cytoplasm. Moreover, the promoter prediction showed a variety of abiotic stresses and phytohormone related -acting elements exist in the 2k up-stream region of . And the evolutionary characteristics of cotton genes were clearly presented by synteny analysis. Moreover, the results of transcriptome and qRT-PCR analysis showed that the expression of were related to the tissue distribution, and further analysis suggested that could respond to various abiotic stress and phytohormonal treatments. Overall, our systematic analysis of genes would not only provide a basis for the understanding of the evolution of , but also found a foundation for the further function analysis of to improve cotton yield and environmental adaptability.