Since 1817, cholera, caused by Vibrio cholerae, has been characterised by seven distinct pandemics. The ongoing seventh pandemic (7P) began in 1961 (1). In this study, we developed a new tool named Multilevel Genome Typing (MGT) for classifying the V. cholerae species with a focus on the 7P. MGT is based on multi-locus sequence typing (MLST), and the concept has been expanded to include a series of MLST schemes that compare population structure from broad to fine resolutions (2). The V. cholerae MGT consists of eight levels, with the lowest, MGT1, composed of 7 loci and the highest, MGT8, consisting of the 7P core genome (3759 loci). We used the MGT to analyse 5771 V. cholerae genomes. The genetic relationships calculated by smaller MGT levels recapitulated previous findings of large-scale 7P transmission across the globe. Furthermore, the larger MGT levels provided an increased discriminatory power to differentiate subgroups within a national outbreak. Additionally, we demonstrated the usefulness of the MGT for non-7P classification, and MGT2 and MGT3 described continental and regional distributions of a large non-7P MGT1 type, respectively. Finally, the MGT described trends in virulency, and 33 MGT STs grouped isolates of the same ctxB, tcpA and ctxB-tcpA genotype. The MGT offers a range of resolutions for typing V. cholerae. The MGT nomenclature is stable, transferable and directly comparable between investigations. The MGT database (https://mgtdb.unsw.edu.au/) can accept and process newly submitted samples. The MGT allows tracking of existing and new isolates, and will be useful for understanding future spread of cholera.