Chrysanthemum is the most economically important medicinal and ornamental plants worldwide. Chuju, a cultivar of Chrysanthemum morifolium, has been widely exploited for drink and medicinal applications, and is ranked the first among the four famous Chrysanthemum plants in China (Xie et al., 2012). However, saline–alkaline soils often lead to plant growth inhibition and yield loss. Here, the main aim of this study tried to increase the tolerance of Chrysanthemum plants to saline–alkaline conditions by application of PGPR. The inoculation of Chrysanthemum plants with Bacillus licheniformis SA03 displayed better growth performance under saline–alkaline stress compared with non-inoculated plants. Moreover, we explored the underlying mechanisms at the physiological and molecular levels responsible for SA03-induced stress tolerance of plants.