Randomly amplified polymorphic DNA (RAPD) has emerged as an effective genetic marker for analysis of Trypanosoma cruzi population variability. This method has been used to study the genetic variability of Mexican T. cruzi stocks and to relate these results to previous classifications. High clonal diversity was observed among the Mexican populations: 24 RAPD types were scored among 56 stocks analyzed. Only two stocks (3.6%) belonged to the T. cruzi II lineage, while all others belonged to T. cruzi I. The robustness of these clusters was statistically highly significant. Mexican T. cruzi I stocks formed a homogeneous group with reduced genetic distances among its members. Parasites from this group were isolated from both domestic and sylvatic cycles over a broad geographic area in Mexico. The two Mexican stocks classified as T. cruzi II (isolated from sylvatic cycles) were of the same RAPD type, although they were not closely related to the three reference T. cruzi II stocks circulating in domestic cycles in Argentina, Brazil, Bolivia, and Chile. These stocks were also unrelated to the formerly named Zymodeme III.Trypanosoma cruzi, the agent of Chagas' disease, which is widely distributed in Latin America, shows considerable genetic polymorphism (14). Extensive studies carried out by using multilocus enzyme electrophoresis have demonstrated that natural populations of T. cruzi have a clonal structure (21), which has led to subdivision of the taxon into two major lineages, T. cruzi I and T. cruzi II (1,13,18,20). Each lineage is genetically heterogeneous, and despite failure to identify subdivisions within T. cruzi I, five subgroups of T. cruzi II have been proposed as discrete typing units (DTU) on the basis of randomly amplified polymorphic DNA (RAPD) analysis (1, 5). These six DTU have been proposed as a reference framework for genetic variability and for biological characterization studies of T. cruzi stocks.A few studies have attempted to characterize Mexican T. cruzi stocks by genetic methods. Seventeen stocks were analyzed using HindIII restriction fragment length polymorphisms associated with rRNA gene spacers and kinetoplast DNA maxicircle polymorphisms (9,12,22). These studies identified two groups of Mexican stocks, which correlate with geographic origin, although assignment to a T. cruzi lineage was not possible. The same stocks were also analyzed by multilocus enzyme electrophoresis, demonstrating a high degree of heterogeneity that was not related to geographic origin (12). Analysis of minicircle kDNA variability among Mexican stocks showed no correlation between the sequence homologies of the hypervariable region of minicircles and clustering (2), contrasting with results obtained for South American stocks (3, 4).In the present study, 56 Mexican stocks, isolated from diverse hosts and with diverse geographic origins, were analyzed by RAPD. Relevant phylogenetic analyses were used to assess population variability and structure, and to evaluate the taxonomic position of Mexican stocks and their corresp...