Microsatellite markers, also called simple sequence repeats (SSRs), are comprised of a 2- to 6-nucleotide repeat motif. They are useful as molecular markers for genetic authentication, crop breeding programs, and linkage analysis for map-based cloning. From a microsatellite-enriched genomic library of Acanthopanax senticosus, we identified 239 new microsatellite-containing sequences. The di-nucleotide repeat units were the most abundant (55.2%), followed by tri-nucleotide repeat units (24.6%). In detailed repeat structures, the $(AG)_n$ motif was most frequent (30.5%), followed by the $(AC)_n$ motif (21.7%). Hepta- and octa-nucleotide repeat motifs were found in each single locus, and a total of 33 (13.8%) complex repeat structures were recorded. This is the first report of mass isolation of microsatellites via screening of an A. senticosus library, and may well provide information useful as a genetic resource for the further study of A. senticosus.