The size polymorphism of nine chromosomes, recognized by specific probes, was analysed in populations of Leishmania (Viannia) braziliensis and L. (V.) peruviana from various Peruvian biogeographical units. Interpretation of the polymorphism, by statistical and phenetic methods, led to the identification of five consensus (α- and β-tubulin) and four variable chromosomes. The dynamics of the variable chromosomes were studied. The promoter role of the environment on their polymorphism was indicated by: (1) the discrimination of L. braziliensis (forest) and L. peruviana (Andes) by the size of the chromosome containing the gp63 genes; and (2) the fact that, within L. peruviana, the polymorphism of the variable chromosomes revealed a strong eco-geographical structuring of parasite populations, accompanied by increasing chromosomal dissimilarity along a cline from north to south. The adaptative significance of the polymorphism of the variable chromosomes was suggested by: (1) a correlation between chromosomal polymorphism and phenotype variability (lesion type in patients and virulence in vitro);, and (2) the association between the decrease in size of the gp63-containing chromosome from L. braziliensis to L. peruviana, and a rearrangement of the gp63 genes, probably accompanied by a decrease in their copy number. As chromosomal variation was shown to be more dependant on eco-geographical differences than isoenzymatic variation, chromosome variation and enzyme variation probably differ in adaptative significance.