Leishmania (Viannia) lainsoni was first described in 1987 in the state of Pará, in the Brazilian Amazon region. The initial characterization of this parasite was performed based only in light microscopy techniques. Posterior studies with this Leishmania species, which focused on biochemistry and molecular assays, showed its divergent position in the Leishmania genus. In this study, we characterize the ultrastructure of culture promastigote forms throughout the growth curve. Our results demonstrate a time-dependent accumulation of electron-dense deposit in the acidocalcisome matrix. We have also analyzed, by transmission electron microscopy, the chronic experimental skin lesion induced in hamster. The experimental infection assay showed adhesion of the intracellular parasites to the parasitophorous vacuole membrane and the occurrence of free vacuoles in the lesion site containing amastigote forms (the amastigote forms morphometrical data were summarized). Our morphological evidences suggest a possible alternative surviving mechanism for L. (Viannia) lainsoni in chronic lesion site.