Increased mortality was observed in a group of 10-day-old ducklings in China in 2010. The dead ducklings were characterized by meningitis, suggesting microbial infection as the cause of disease. Laboratory investigation led to the isolation of a bacterial strain designated as AL101002 from the brain of dead ducklings. Subsequent experimental infections with this strain resulted in marked symptoms in the ducklings similar to those observed in nature outbreaks. Gram-staining revealed Gram-positive cocci in pairs or short chains. Phenotypical analysis revealed the microorganism as Streptococcus pasteurianus. DNA sequencing revealed that the isolate was Streptococcus gallolyticus subsp. pasteurianus. Experimental infection with AL101002 resulted in the death of ducklings with meningitis. To the best of our knowledge, this is the first report of the isolation of S. gallolyticus subsp. pasteurianus with high virulence in ducklings.