The study was taken up with the objective of evaluating the bacterial endophytes isolated from tomato towards seedling growth promotion and organic seedling production. Five isolates from tomato cv. Arka Vikas (Pseudomonas oleovorans, Stenotrophomonas maltophilia, Bacillus pumilus, Agrobacterium tumefaciens, and Microbacterium pumilum) and nine isolates from cv. Arka Abha (P. oleovorans, Pseudomonas plecoglossicida, Pantoea ananatis, Citrobacter freundii, Staphylococcus hominis, Sphingobacterium multivorum, Enterobacter cloacae, Arthrobacter globiformis, and A. tumefaciens) isolated from the root tissue of 4-week-old seedlings were tested for the plant growth promotion (PGP) characteristics and the effect on seedling growth. Most isolates showed ammonia and indole production, while five isolates (one from Arka Vikas and four from Arka Abha) displayed phosphate solubilization capability. Following seed fortification (soaking seeds in 0.1 OD600nm bacterial suspension for 1 h), several isolates displayed improved seed germination and/or higher seedling vigor in paper towel and glasshouse trials. Two isolates of P. oleovorans (Tm-Av01 and Tm-Ab01 from Arka Vikas and Arka Abha, respectively) and one A. tumefaciens isolate (Tm-Ab09) from Arka Abha showed higher seedling vigor index over control in both cultivars. The two isolates Tm-Av01 and Tm-Ab01 (P. oleovorans) which formed the predominant natural endophyte in the respective hosts with the additional feature of high antagonistic activity against the bacterial wilt pathogen, Ralstonia solanacearum, have been identified as promising endophytes towards seedling growth enhancement and organic seedling production across both the cultivars.