In this study, the alpha-galacturonosyltransferase (GAUT) family genes in the whole genome of Gossypium barbadense were identified and bioinformatics and the expression analysis during fiber development were carried out. The results showed that a total of 37 GAUT genes were systematically identified from G. barbadense and classified into three subfamilies. They were distributed over 18 chromosomes of G. barbadense and had four conserved motifs. A majority of GAUT protein were located in the cytoplasm. According to the change of the GAUTs expression at different stages of fiber development, they were divided into four expression patterns including high expression pattern of initial stage, high expression pattern of fiber elongation stage, high expression pattern of secondary wall thickening period and low expression pattern in the whole period. GAUT05, GAUT06, GAUT07, GAUT23, GAUT24, GAUT26 might play important roles in fiber development based on the expression of GAUT gene family. These results provide a useful reference for the study of the function of the GAUT gene family in the development of fiber in G. barbadense.