The discovery of novel biocontrol agents requires the continuous scrutiny of native microorganisms to ensure that they will be useful on a regional scale. The goal of the present work was to discover novel antagonistic bacteria against
Fusarium oxysporum
ff. spp.
lycopersici
race 3 (
Fol
R3) and
radicis-lycopersici
(
Forl
) causing
Fusarium
wilt disease and
Fusarium
crown and root rot of tomatoes, respectively. High-throughput liquid antagonism screening of 1,875 rhizospheric bacterial strains followed by dual confrontation assays in 96-well plates was used to select bacteria exhibiting > 50% fungal growth inhibition. In a second dual confrontation assay in 10-cm Petri dishes, bacteria showing > 20%
Fol
R3 or
Forl
growth inhibition were further screened using a blood hemolysis test. After discarding β-hemolytic bacteria, a seedling antagonistic assay was performed to select five potential antagonists. A phylogenetic analysis of 16S rRNA identified one strain as
Acinetobacter calcoaceticus
(
Ac
DB3) and four strains as members of the genus
Bacillus
(
B. amyloliquefaciens Ba
MA26,
Bacillus siamensis Bsi
DA2,
B. subtilis Bs
TA16 and
B. thuringiensis Bt
MB9). Greenhouse assays demonstrated that
Bs
TA16 and
Ac
DB3 were the most promising antagonists against
Fol
R3 and
Forl
, respectively. Pathogen biocontrol and growth promotion mechanisms used by these bacteria include the production of siderophores, biofilm, proteases, endoglucanases and indole acetic acid, and phosphate solubilization. These five bacteria exerted differential responses on pathogen control depending on the tomato hybrid, and on the growth stage of tomatoes. We report for the first time the use of an
Acinetobacter calcoaceticus
isolate (
Ac
DB3) to control
Forl
in tomato under greenhouse conditions.