Salinization of the soils is one of the most prominent problems threatening global food security. Root microbiome engineering using biofertilizers provides a sustainable way to increase agricultural productivity. Halophytes, which are extremely salt-tolerant plants, can tolerate up to 1300 mM NaCl. Members of the halophytic root microbiome now provide a promising solution to meet the increased demand in the agricultural output. Here, we explore the members of this microbiome and explain the plant growth-promoting functions of them. We discuss the manipulation of the root microbiome with synthetic microbial communities including keystone microorganisms of the halophytic root microbiome. Importantly, we provide a simple method in R software to find these putative keystone taxa using network analysis. We believe this strategy will provide a valuable tool for future studies performing the combined investigation of the root bacteria and fungi of halophytes.