We review and discuss here the specificity and contribution of genome (re-)arrangement studies for the exploration of genetic diversity among Leishmania. We show how the early molecular karyotyping studies generated an original perception of the genetics and evolution of these Protozoa, while providing some possible explanations on the parasite diverse phenotypes (drug resistance, pathogenicity...). We compare the results with the enormous amount of data provided by the recent genome sequencing projects, so far focused on one strain per genus/species. We highlight the relevance of parallel sequencing of different strains of a same species, now made possible by the new sequencing technologies. We recommend paying a particular attention to variation in gene copy number, a feature showed by the karyotyping studies to be extremely informative.