The effects of cell-free supernatants (S) and anionic fractions (Q) from three different strains of Bacillus subtilis were evaluated on weed seed germination. The plant growth promoting rhizobacteria (PGPR) strains DN and Car13, as well as a non-promoting strain (PY79), were tested on pigweed (Amaranthus hybridus L.) and Johnson grass (Sorghum halepense L. pers). The application of anionic fractions QCar13, QDN and QPY caused a drastic decrease in the germination rates of both pigweed and Johnson grass seeds relative to controls. These results suggest the presence of one or several metabolites capable of inhibiting germination in both weeds, while acting more effectively on dicotyledonous seeds. This work shows the potential of essayed fractions in weed control.