The inbreeding effective population size is an estimate of inbreeding and genetic drift in populations. It is an important tool for conservation genetics because it represents the number of individuals that are effectively contributing alleles to the subsequent generations. Several studies have been published in the last decades on the genetic structure of natural plant populations of the Cerrado, the Central-Brazilian savannahs, but most of them do not present effective size estimates. The objective of this study was to show such estimates for Solanum lycocarpum, a Cerrado species that is in danger of genetic erosion. We utilized microsatellites, isozymes, and 2 natural populations for each marker to estimate the population inbreeding effective size of a group of populations (N^e(v)) and the minimum number of populations that should be conserved (S^(ref)) in order to retain an effective number of 500. For the 2 markers that were utilized, only approximately 12% of the individuals are effective in the populations. The value obtained for S^(ref) was approximately 80.