Leishmaniasis is a complex of diseases caused by protozoan parasites of Leishmania genus, endemic in Brazil and in countries of the old and new worlds. The clinical manifestations of the disease depend on the infectivity of the species involved and the host immune response. Leishmania (Leishmania) infantum is associated with the visceral form of the disease in humans and dogs, but some studies evidence the potential of visceralization of Leishmania (L.) amazonensis. It is known that these trypanosomatids have great potential of adaptability in the face of the most adverse environmental conditions. The biological cycle of these parasites can undergo changes due to the environment in which they are exposed and, mainly, by anthroponotic changes in the ecosystem. The survival and perpetuation of Leishmania are related to modifications at genetic level, which can modify its gene expression. Hence, there is great relevance in employing field samples from hosts, such as dogs and humans, from endemic areas for visceral leishmaniasis (VL), where parasites certainly undergo environmental pressures and can alter their genomic content and eventually their gene expression due to reservoirs, vectors and hosts availability. This work aims at performing a comparative analysis of Leishmania infantum isolates, predominantly from naturally infected dogs from different states of Brazil – Bahia, Minas Gerais (Januária and Governador Valadares cities), Rio Grande do Norte (RN) and Santa Catarina (SC). By applying bioinformatic tools, 85 genomes were analyzed for variation of chromosome copy number and SNVs, phylogeny, population structure and gene enrichment. The SNPs and phylogeny analyses indicated a pattern of clusterization by endemic region. Intra and interpopulation variations were observed among the isolates. Januária isolates formed two well defined clades, one with rural and the other with urban isolates, suggesting that distinct transmission cycles are occurring in the area. Also, isolates from Januária and RN have little intra and interpopulation variability; Governador Valadares and SC isolates have a higher frequency of heterozygous genotypes when compared to Januaria and RN isolates. In addition, in silico analyses also revealed aneuploidies more evident on chromosomes 8, 23 and 31, which contain enriched genes related to the metabolic activities, survival and virulence of the parasites. This study suggests that genomic surveillance of Leishmania is of great relevance for a better understanding of disease dynamics in endemic regions.