Microsatellites are now firmly established as an informative marker system, with increasing popularity as a tool amongst molecular ecologists. We have developed a method of constructing an enriched microsatellite library for the tropical tree species Swietenia humilis Zucc. (Meliaceae). This method is based on a precloning enrichment of SSRs using synthetic oligonucleotide probes, bound to magnetic beads and hybridizing to complementary microsatellite core sequences in digested genomic DNA. Here we describe the isolation and characterization of 10 microsatellite loci that have been used to survey the genetic diversity within a natural population of S. humilis. A total of 97 alleles were identified with an average of 9.7 alleles over all loci. Very high levels of allelic polymorphism were detected at individual loci, with 23 alleles observed at the most variable. The mean observed heterozygosity was 0.415 (range 0.038-0.815) exceeding levels of diversity detected in related species which used isozymes as the marker system. Subpopulation differentiation at a microgeographical scale was low (FST= 0.036) and the values of Nm, calculated from the allelic frequencies, were greater than 1 thus reflecting the extent of gene flow occurring between individual trees.