Biochar (the solid co-product of biomass pyrolysis), has several agronomic benefits in soil and has a great potential as a supplemental amendment in soilless and nursery media. As biochar has a significant influence on the severity of foliar and soilborne diseases in various crops, its influence on young seedlings health and the potential mechanisms involved in the process has to be studied. This study tested i) the impact of biochar on pre-emergence damping-off caused by Pythium aphanidermatum and ii) biochar's influence on soil bacterial community composition and diversity. We found that biochar suppressed pre-emergence damping-off by up to 76%. PCR-DGGE analyses of the 16S rRNA gene showed substantial differences in bacterial composition between biochar amended and control soils. Illumina sequencing revealed a significant enrichment of bacterial abundance, potentially beneficial microorganisms and shift in microbial community structure. These changes may play an important role in the overall effects of biochar on disease suppression either through direct antagonist effect towards pathogen or indirectly via induction of systemic resistance in the plant.