Paenibacillus sp. JZ16 is a gram-positive, rod-shaped, motile root endophytic bacterium of the pioneer desert halophytic plant Zygophyllum simplex. JZ16 was previously shown to promote salinity stress tolerance in Arabidopsis thaliana and possesses a highly motile phenotype on nutrient agar. JZ16 genome sequencing using PacBio generated 82,236 reads with a mean insert read length of 11,432 bp and an estimated genome coverage of 127X, resulting in a chromosome of 7,421,843 bp with a GC content of 49.25% encoding 6710 proteins, 8 rRNA operons, 117 ncRNAs and 73 tRNAs. Whole-genome sequencing analysis revealed a potentially new species for JZ16. Functional analysis revealed the presence of a number of enzymes involved in the breakdown of plant-based polymers. JZ16 could be of potential use in agricultural applications for promoting biotic and abiotic stress tolerance and for biotechnological processes (e.g., as biocatalysts for biofuel production). The culture-dependent collection of bacterial endophytes from desert plants combined with genome sequence mining provides new opportunities for industrial applications.