Accurate identification of bacterial species is critical for epidemiologic, phylogenetic, and diagnostic purposes. The classification of leptospires has undergone several changes following the discovery of the leptospirosis agent more than a century ago. With the genomic era, the number of described Leptospira species has more than doubled in recent years. Genotyping, including whole-genome-based typing, allows discrimination of isolates at the subspecies level. Access to genomes has also facilitated the study of gene repertoire and virulence-associated factors. Herein we review the taxonomic classification of the genus Leptospira and highlight recent findings based on the analysis of genomes.