Leptospirosis, caused by pathogenic Leptospira spp., is one of the most prevalent zoonotic diseases worldwide. While whole genome sequencing (WGS) has revealed global genetic diversity of Leptospira spp., large-scale genomic comparisons between human and animal isolates remain limited, and their epidemiological relationships are not fully understood. In this study, we performed WGS on 204 Leptospira isolates obtained from humans, dogs, and wild or feral animals in Japan between 1989 and 2021. Among these, 146 isolates of L. interrogans—the most frequently isolated Leptospira species with epidemiological relevance—were analyzed using Bayesian analysis of population structure (BAPS) and core genome multilocus sequence typing (cgMLST). These strains were classified into 30 clonal groups (CGs), including 26 novel CGs. Each CG consistently corresponded to a single serogroup, highlighting the potential of cgMLST for serogroup prediction. BAPS analysis revealed that serogroup Hebdomadis—particularly clades Li20 and Li13—predominated among human infections on islands of Okinawa Prefecture. Li20/CG486 strains were also isolated from mongooses and Ryukyu mouse, suggesting that these animals may serve as reservoirs. Li3/CG6 strains of serogroup Icterohaemorrhagiae were detected in both humans and brown rats in urban areas, underscoring the role of rats in transmission. Several canine isolates shared CGs with wildlife: Li20/CG481 with mongooses, Li20/CG486 with raccoons, Li6/CG485 with brown rats, and Li20/CG470 with large Japanese field mice, supporting environmental exposure as a likely route of canine infection. These findings demonstrate the utility of cgMLST and BAPS for high-resolution genotyping and emphasize the need for monitoring native and introduced wildlife to better understand and control leptospirosis in Japan.