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Salicornia bigelovii is a novel crop for salty soils, which can contribute to arid-zone management where irrigation with salty water, including sea water, is now a necessity. Nitrogen fixation by bacteria associated with the roots of S. bigelovii and similar halophytes is an important source of available nitrogen in salt marsh ecosystems. However, the diversity of the rhizosphere of Salicornia is unknown. Five areas around the Bay of La Paz in Baja California Sur, Mexico were sampled to detect nitrogen-fixing bacteria associated with this halophyte; from these, 18 colonies were isolated. Only one showed high acetylene reduction activity. This bacterium was identified as Klebsiella pneumoniae. The effects of K. pneumoniae were evaluated at the germination and early seedling growth stages of two genotypes of S. bigelovii (’wild genotype’ and cultivar SOS-10), as an alternative crop for semiarid and saline environments. This bacterium, in conjunction with Azospirillum halopraeferens, was tested for growth-promoting ability when inoculated on S. bigelovii genotypes under various saline concentration conditions. During germination and early seedling growth, K. pneumoniae showed high specificity for the wild S. bigelovii genotype, while A. halopraeferens was more specific for the improved S. bigelovii genotype SOS-10. This is the first report of K. pneumoniae as a nitrogen-fixing bacterium associated with the oilseed S. bigelovii, a novel halophyte crop. A reliable biological method, based on beneficial bacteria, is suggested to help maintain or improve the fertility of soils sustaining Salicornia fields.