Genetic variability among Taenia solium isolates was studied in 160 cysticerci from 6 pigs, 4 from Mexico, 1 from Honduras, and 1 from Tanzania. Random amplified polymorphic DNA (RAPD) analysis performed with 4 commercial primers showed 88% polymorphic loci and an average heterozygosity of 0.077; however, several alleles were fixed within each isolate. Linkage disequilibrium analysis indicated that 3 of the 6 isolates had a random association of alleles, whereas the other 3 had a clonal structure. These results suggest the existence of local lineages in T. solium, with events of genetic recombination within them.