A methodological approach is proposed to select rapidly DNA sequences characterized by a well defined specificity and potentially interesting to be used as diagnostic probes or as taxonomic and phylogenetic markers. A fragment amplified from a diversified sample of Trypanosoma cruzi stocks by the RAPD (random amplified polymorphic DNA) method with the A8 primer, previously found to be monomorphic in all stocks, was separated in 2 fragments using polyacrylamide electrophoresis. RFLP (restriction fragment length polymorphism) analysis of the 750-bp fragment common to all stocks revealed some sequence heterogeneity within the T. cruzi species, whereas hybridization experiments showed a high homology between fragments amplified from different T. cruzi stocks. These results suggest that sequence analysis will allow the design of internal primers to be used as probes to target specific taxonomic levels (clone, family of related clones, or species) and for diagnosis.