Thirty-six Trypanosomatidae stocks isolated from various hosts and geographical areas in Colombia and 7 others from Bolivia, Chile, Honduras and Panama have been surveyed by Multilocus Enzyme Electrophoresis (MLEE). Part of the Colombian stocks were previously characterized by morphology and biological behavior as belonging to Trypanosoma cruzi and Trypanosoma rangeli taxa, others were unknown species. The genetic variability observed at 13 different loci was considerable, since 38 zymodemes could be distinguished and 2 upper branches were observed. The first branch corresponded to T. cruzi and was divided in the two major phylogenetic subdivision of T. cruzi (T. cruzi I, T. cruzi II). The majority of the Colombian T. cruzi stocks (92%) felt into T. cruzi I. Only two stocks, isolated from sylvatic mammals, belonged to T. cruzi II. Among T. cruzi I, we did not observed any additional phylogenetic subdivision and host-dependent genotype specificity. The second branch was genetically very heterogeneous and included all T. rangeli stocks, the stocks isolated from bats and one stock isolated from a sylvatic R. prolixus vector. The stocks belonging to T. rangeli presented only one locus instead of two for the malic enzyme system. Since, the upper level of resolution of the isoenzyme method was exceeded, the current clustering study failed to draw a clear distinction between such a diverse set of Trypanosomatidae species.