The heat shock protein 90 (HSP90) family members are widely involved in the growth and development of organisms as well as the transmission of stress signals. They are of significant importance in the study of signal transduction, cell cycle regulation, protein degradation and transport. In order to decipher the HSP90 gene family in foxtail millet (Setaria italica（L.）P. Beauv.), and identify their elite haplotypes being important in drought tolerance, the family members (referred SiHSP90s) were identified by taking use of the foxtail millet genome reference. Nine SiHSP90s members were identified on 5 chromosomes, with the intron number of 1 to 19, and the amino acids of deduced protein ranged from 404 to 818. Phylogenetic analysis suggested that SiHSP90s were divided into four groups. SiHSP90s were predicted to be localized in cytoplasm and endoplasmic reticulum. Based on the released foxtail millet transcriptome data, the transcriptional patterns of SiHSP90s in tissues were different. Nine stress and hormone regulatory elements were predicted via cis-acting element analysis, indicating that the transcriptional reprogramming of SiHSP90s under different abiotic stresses might be present. Haplotype analysis of 532 foxtail millet varieties showed little variation in gene region but abundant variations in the promoter region, which enables defining four haplotypes. In conjugation with phenotypic analysis, it is found that the haplotype H004 is likely the most elite haplotype showing drought tolerant, possibly due to the core sequence variations of this haplotype at cis-acting element responding to the Methyl Jasmonate (MeJA) treatments.