Along long-term evolution, plants have developed some flexible mechanisms to adapt to adverse environments (Marschner and Römheld, 1994; Chen et al., 2010; Li et al., 2016). It is one of important strategies to attract colonization of diverse beneficial microbes in the rhizosphere of host plants (Lebeis et al., 2015). It is widely recognized that the complex mutualistic interactions can assist plants to cope with unfavorable conditions (Ait Barka et al., 2006; Mishra et al., 2014; Sukweenadhi et al., 2015). Recently, numerous studies have indicated that PGPR confers increased tolerance of plants to various abiotic stresses including drought, salinity, and nutrient deficiency (Dey et al., 2004; Scholz et al., 2011; Zhou et al., 2016a,b). However, whether PGPR could induce saline–alkaline tolerance in plants and the underlying mechanisms remain elusive. We reported here for the first time that Chrysanthemum plants inoculated with B. licheniformis SA03 were greater resistant to saline–alkaline conditions, as evidenced by lower biomass loss and higher survival rates. Moreover, transcriptomic, biochemical, and pharmacological analyses were combined to unravel the mechanisms behind SA03 activated the adaptive responses of plants to saline–alkaline conditions. Our results revealed that the SA03-induced ABA accumulation was required for the tolerance of plants to saline–alkaline stress, indicating that the increased ABA level was a primarily acting mode of SA03 to regulate saline–alkaline stress response in plants.