In this study, we have analysed enzyme polymorphism among a group of protozoan parasites of the genus Endotrypanum (Kinetoplastida: Trypanosomatidae). Seventeen stocks of Endotrypanum spp. isolated from sloths (Choloepus didactylus and C. juruanus) in the Amazon Region of Brazil were analysed by enzyme electrophoresis, and their electromorphic profiles were compared with reference strains reported previously. The 16 enzymic loci were analysed, and the strains were classified into zymodemes, each representing parasites with unique enzyme profiles. Each zymodeme was considered as an elementary taxon, and using numerical analyses (cladistic, agglomerative hierarchical and ordination techniques) the genus was shown to be monophyletic and the 12 zymodemes characterized could be divided into 3 groups (A, B, C). The heterogeneous population (which may represent a complex of parasite species or strains variants) showed, however, no correlation with the origin (i.e. host species involved or geographic area of isolation) of Endotrypanum stocks. Eight isolates of Endotrypanum sp. from Rondonia State (Brazil) and a parasite strain from Panama were clustered together into a zymodeme, which was phenetically closely related to the E. monterogeii from Costa Rica. The data indicate that E. schaudinni is a species complex.