Plant root microbiome, a community of bacteria living in close association with plant root, plays a significant role in plant health and productivity. How their functions contribute to plant growth are not well-understood. We hypothesized that phenotyping multiple in vitro functions of the culturable root endophytic bacteria could predict their impact on in planta growth. 183 bacterial endophytes were isolated from the roots of field-grown domesticated tomato species and its wild cousin. 30 isolates from each genotype were screened for four in vitro functional traits: production of auxin and siderophores, phosphate solubilization, and direct antagonism to a soilborne bacterial pathogen of tomato, Ralstonia solanacearum. Biosynthesis genes of DAPG or HCN were also screened for their presence in the genome of the isolates. Hierarchical clustering of the in vitro functional traits suggested the isolates was clustered into four distinctive groups: auxin producers, phosphorus solubilizer, siderophore producer, and a group with high antagonism against R. solanacearum. Auxin producers tended to have low antagonistic traits. Isolates with the DAPG biosynthesis gene also tended to be strong siderophore producers. Two isolates from each of the functional group were then individually inoculated on plants. Preliminary results suggested that isolates with similar in vitro functional traits performed similarly in plants. Understanding how in vitro functional traits of bacteria relate to their impact on plants potentially offer a powerful strategy for further microbiome modeling studies.