NAC transcription factors have been found to play an important role in several plant development programs and stress responses. In this study, a NAC gene, ClNAC9 (Chrysanthemum lavandulifolium NAC gene), was isolated from a cDNA library constructed according to the known expressed sequence tag sequence. The cDNA full-length sequence of ClNAC9 is comprised of 881 bp, encoding a putative protein of 217 amino acids. ClNAC9 has a conserved NAC domain in the N-terminus — the NAM domain. ClNAC9 is highly similar to other NACs, especially SENU5 subgroup members. Transgenic Arabidopsis overexpressing ClNAC9 controlled by the CaMV-35S promoter was generated and subjected to saline, alkaline, and drought stresses for morphological and physiological assays. Morphological analyses showed that transgenic plants had enhanced tolerance to saline, alkaline, and drought stresses, as indicated by improved physiological traits, including higher superoxide dismutase and peroxidase activities, and reduced malondialdehyde accumulation. Moreover, overexpression of ClNAC9 enhanced up-regulation of RD29A, RD26, MYB2, and MYB96 expression, and reduced HAB1 expression under saline, alkaline, and drought treatments. Taken together, our results demonstrate that ClNAC9 is likely related to saline, alkaline, and drought resistances and overexpression of ClNAC9 increases the saline, alkaline, and drought resistance of transgenic Arabidopsis.