Acute graft-versus-host disease (aGVHD) is one of the major causes of death after allogeneic hematopoietic stem-cell transplantation (allo-HSCT). Recently, aGVHD onset was linked to intestinal microbiota (IM). However, other bacterial-rich gastrointestinal sites, such as the mouth, which hosts several distinctive microbiotas, may also impact the risk of GVHD. The dental biofilm microbiota (DBM) is highly diverse and, like the IM, interacts with host cells and modulates immune homeostasis. We characterized changes in the DBM of patients during allo-HSCT and evaluated whether the DBM could be associated with the risk of aGVHD. DBM dysbiosis during allo-HSCT was marked by a gradual loss of bacterial diversity. We observed significant changes in DBM genera composition, with a decrease in the abundance of commensal genera, and overgrowths of potentially pathogenic bacteria. High Streptococcus and high Corynebacterium relative abundance at preconditioning were associated with higher risk of aGVHD (67% vs. 33%; HR = 2.89, P = 0.04 and 73% vs. 37%; HR = 2.74, P = 0.04, respectively), while high Veillonella relative abundance was associated with a lower risk of aGVHD (27% vs. 73%; HR = 0.24, P < 0.01). Enterococcus faecalis bloom was observed in 20% of allo-HSCT recipients' DBM and was significantly associated with a higher risk of aGVHD (100% vs. 40%; HR = 4.07, P < 0.001) and severe aGVHD (60% vs. 12%; HR = 6.82, P = 0.01). To the best of our knowledge, this is the first study demonstrating that DBM dysbiosis is associated with the aGVHD risk after allo-HSCT.