Collecting germplasm to broaden breeding resources is an essential activity of genebanks. Research to understand how genetic diversity is partitioned in nature might help to identify collections rich in diversity. Previous studies among wild populations of Solanum fendleri (a disomic polyploid selfer) and S. jamesii (a diploid outcrosser) revealed no significant associations between genetic and ecogeographic variation. Even physical separation did not predict genetic differences. In this study, 28 populations of S. sucrense Hawkes (2n=4x=48), a Bolivian species with another breeding system (polysomic polyploid oucrosser), were evaluated. The objective was to assess whether genetic differences between populations are predicted by differences in geographic parameters at the natural site of origin. Genetic differentiation was estimated by using 216 RAPD markers. The average genetic distance (GD) found between pairs of populations was 31% (ranging from 8% to 44%). Correlations of GD with latitude, longitude, altitude and distance were not significant. Multiple regression analysis also confirmed that GD was not explained by the geographic parameters used. We conclude that geographic origin data is not very useful in gauging interpopulation genetic diversity in the genebank.