DNA samples of the spectacled bear (Tremarctos ornatus) from five Andean countries, Venezuela, Colombia, Ecuador, Peru and Bolivia, were analyzed for nine microsatellite loci. Seven of them were polymorphic, which led us to investigate several population-genetic parameters. Private alleles and significant differences in gene frequencies were found among the populations studied, which demonstrated the extent of genetic differentiation among the spectacled bear populations. The levels of gene diversity measured with these microsatellites were rather modest in this species. Hardy-Weinberg disequilibrium was especially found for the overall and the Ecuadorian samples, and might be due to the Wahl-und effect or consanguinity. Significant genetic heterogeneity was mainly observed among the Colombian and the Ecuadorian populations. Markov chain Monte Carlo simulations clearly showed that two different gene pools were present, one present in the Venezuelan-Colombian bears and other in the Ecuadorian ones.