Capnocytophaga canimorsus and C. cynodegmi are gram negative bacteria that can be transmitted to humans from dogs or cats and cause serious infections. Routine bacteriological methods, including fermentation and phenotypic tests are insufficient to correctly identify C. canimorsus or C. cynodegmi. The aim of this study was to evaluate the performance of VITEK2 and MALDI-TOF in identification of these bacteria. Twenty two isolates that were identified as C. canimorsus / C. cynodegmi by 16S rRNA sequencing were included in the study and were further investigated with VITEK2 and MALDI-TOF. A Capnocytophaga species-specific PCR was used as the reference method. Out of 22 included isolates, the species-specific PCR identified six blood isolates as C. canimorsus and 14 wound isolates as C. cynodegmi. Two isolates could not be identified with the reference method. VITEK2 identified 10/20 isolates correctly to Capnocytophaga spp. MALDI-TOF analysis correctly identified 6/6 C. canimorsus and 13/14 C. cynodegmi isolates. The mean time to identification with VITEK2 was 6 hours whereas MALDI-TOF required approximately 10 minutes per sample. Here we show that MALDI-TOF rapidly identified C. canimorsus and C. cynodegmi and thus constitutes a valuable diagnostic tool in the clinical laboratory.