A novel strain of the genus Pseudomonas was isolated from a high-altitude volcano in Toluca, Mexico. This isolate, initially named Ps4, could grow well at 4 °C making it a psychrotolerant bacterium. Previous characterization of Ps4 revealed interesting characteristics related to plant growth promotion, including auxin production, siderophores, and phosphate solubilization capacity. In this work, the ability of Ps4 to stimulate the early development of Capsicum annuum plants without signs of phytopathogenicity was proven. A thorough whole genome analysis determined that isolate Ps4 belongs to the Pseudomonas fluorescens species complex, and specifically to the species P. marginalis with a Mash distance of 0.0118927 to the closest reference genome (RefSeq: GCF_007858175.1). The phylogenomic evidence allowed us to establish that it is a new strain denoted as P. marginalis BMH-2007. Noticeably, its genomic features were consistent with plant-growth promotion traits, we observed coding sequences for IAA biosynthesis, iron and phosphate transport, among others. As it is a species associated with phytopathogenicity, the virulence factors encoded by the genome were analyzed, which revealed the presence of a type VI secretion system, associated both with biological control and plant-growth promotion.