This case report describes a 60-year-old man who presented with septic shock. A novel whole genome next-generation sequencing assay identified Capnocytophaga canimorsus in the patient's plasma within 24 hours, providing a presumptive diagnosis. Conventional blood cultures later grew C. canimorsus and 16S rRNA sequencing confirmed the identification after multiple attempts. This demonstrates the potential of next-generation sequencing to rapidly diagnose infections caused by fastidious pathogens directly from patient samples.