We describe the sequences of six primer pairs for the PCR amplification of nuclear microsatellite markers in the tree shrews, Tupaia glis and T. belangeri. Multilocus genotyping based on non-destructive DNA sampling of live-trapped animals reveals high allelic variability (A) and heterozygosity (H e ) at these loci. Such characteristics make these genetic markers ideal for linkage mapping and comparative genomics, and for studies of pedigree relationships, population structure, and population genetic variability in wild populations. We illustrate another use of these markers in the study of genetic erosion in small recently fragmented natural populations of tree shrews in south Thailand. This method for detecting and monitoring genetic erosion in fragmented populations can be applied to larger taxa of traditional concern to wildlife managers.