Two stocks and nine clones of trypanosomes of the subgenus Schizotrypanum were analyzed based on their electrophoretic pattern of EcoR1 digestion products of kinetoplast DNA (k-DNA) minicircles (schizodeme) and isoenzymes (zymodeme). The trypanosome stocks were isolated from Phyllostomus hastatus bats collected in different locations in Minas Gerais State, Brazil. The k-DNA pattern showed major variations between stocks and microvariations among the clones. Furthermore, in one of several cloning attempts, two different populations could be isolated. Among the six enzymes studied, glucose phosphate isomerase presented different patterns for stocks and clones. No similarity was found among bat trypanosomes and Trypanosoma (Schizotrypanum) cruzi standard zymodemes. This shows that bat trypanosomes are distinct from T. (S.) cruzi.