The genetic structure of two populations of Naegleria lovaniensis, comprising 71 isolates collected from the same local geographical area was investigated by isoenzyme analysis. Allelic variation at seven polymorphic enzymatic loci allowed identification of 45 distinctive genotype associations. Analysis of single locus variation reveals that most of them are close to Hardy-Weinberg equilibrium, which indicates segregation and free recombination between alleles. The recovery of a relatively high number of distinct genotypic associations (most of them being unique), and the absence of linkage disequilibrium between genotypes at the different loci also support the existence of recombination. Although we have no idea about the process involved, the results clearly indicate that genetic exchanges occur, at least occasionally, in natural populations of N. lovaniensis.