Two trypanosome clones, representing East and West African homozygotes at 2 isoenzyme loci (T. b. rhodesiense MHOM/ZM/74/58 [CLONE B] and T. b. brucei MSUS/CI/78/TSW 196 [CLONE A]), were cotransmitted through tsetse flies and the resulting trypanosome populations checked for the presence of non-parental karyotypes by pulsed-field gel electrophoresis. Ten clones isolated from these populations proved to have 5 different recombinant genotypes by analysis of nuclear and kinetoplast DNA (kDNA) polymorphisms. It is inferred that genetic exchange occurred between the 2 trypanosome clones in the fly, as previously reported for 2 other T. brucei spp. clones by Jenni and colleagues. For the most part, the hybrid clones shared many characteristics with both parents and their genotypes were consistent with segregation and reassortment of parental alleles. The least amount of genetic material exchanged was kDNA alone. Regarding the mechanism of genetic exchange, several hybrid clones had identical and unique nuclear DNA polymorphisms, but different kDNA type. Assuming that the same reassortment of nuclear markers is unlikely to occur by chance, these clones most probably arose from a predecessor carrying both types of kDNA.