The Andean (spectacled) bear (Tremarctos ornatus) is the only extant species of bear in South America. This species is considered Vulnerable by the International Union for Conservation of Nature (IUCN), although current population sizes are unclear. To study Andean bears using DNA and non-invasive sampling, we screened 13 microsatellite loci using DNA extracted from blood, saliva, hair, and feces from 16 captive bears. Polymorphic loci were tested with samples from wild bears using DNA extracted from hair and feces collected in the Oyacachi territory inside the Cayambe-Coca Reserve in Ecuador during 2000 and 2001. Ten loci produced reliable results and were polymorphic with a mean of 4 alleles/locus. A minimum of 7 loci were needed for individual identification of wild bears using a probability of identity for siblings P_ID(sib) threshold of <0.01. Andean bears in the Oyacachi territory had moderate levels of genetic diversity (expected heterozygosity, H_E  =  0.45). Although genotyping success rates were low in this pilot study, noninvasive genetic sampling of Andean bear hair and feces provides a useful alternative method for studying this species. When launching a project to census wild animals using hair or fecal samples, we recommend re-evaluating at least the 9 most informative microsatellite loci (G10M, UarMu50, G10H, G10B, G10J, G10X, G10P, G10O, and CXX20), recalculating probability of identity (P_ID) values and considering genotyping error rates.