Widespread use of the herbicide glyphosate in agriculture has resulted in serious environmental problems. Thus, environment-friendly technological solutions are urgently needed for the removal of residual glyphosate from soil. Here, we successfully isolated a novel bacterial strain, Chryseobacterium sp. Y16C, which efficiently degrades glyphosate and its main metabolite aminomethylphosphonic acid (AMPA). Strain Y16C was found to completely degrade glyphosate at 400 mg·L concentration within four days. Kinetics analysis indicated that glyphosate biodegradation was concentration-dependent, with a maximum specific degradation rate, half-saturation constant, and inhibition constant of 0.91459 d, 15.79796 mg·L, and 290.28133 mg·L, respectively. AMPA was identified as the major degradation product of glyphosate degradation, suggesting that glyphosate was first degraded via cleavage of its C-N bond prior to subsequent metabolic degradation. Strain Y16C was also found to tolerate and degrade AMPA at concentrations up to 800 mg·L. Moreover, strain Y16C accelerated glyphosate degradation in soil indirectly by inducing a slight alteration in the diversity and composition of soil microbial community. Taken together, our results suggest that strain Y16C may be a potential microbial agent for bioremediation of glyphosate-contaminated soil.