In this study, we characterize a panel of 20 microsatellite markers that reproducibly amplify in Azara's owl monkeys (Aotus azarai) for use in genetic profiling analyses. A total of 128 individuals from our study site in Formosa, Argentina, were genotyped for 20 markers, 13 of which were found to be polymorphic. The levels of allelic variation at these loci provided paternity exclusion probabilities of 0.852 when neither parent was known, and 0.981 when one parent was known. In addition, our analysis revealed that, although genotypes can be rapidly scored using fluorescence-based fragment analysis, the presence of complex or multiple short tandem repeat (STR) motifs at a microsatellite locus could generate similar fragment patterns from alleles that have different nucleotide sequences and perhaps different evolutionary origins. Even so, this collection of microsatellite loci is suitable for parentage analyses and will allow us to test various hypotheses about the relationship between social behavior and kinship in wild owl monkey populations. Furthermore, given the limited number of platyrrhine-specific microsatellite loci available in the literature, this STR panel represents a valuable tool for population studies of other cebines and callitrichines.