• Premise of the study: The first microsatellite primers were developed for Protium subserratum, a widespread Amazonian tree, to investigate genetic differentiation between populations found on clay, brown-sand, and white-sand soils. • Methods and Results: Seventeen primer pairs were identified from two individuals of P. subserratum found on white-sand and brown-sand soil types. Polymorphism was analyzed in 63 individuals from a total of three populations, each found on a different soil type. The primers amplified tetra-, tri-, and dinucleotide repeats with three to 24 alleles per locus. Excluding monomorphic loci, observed and expected heterozygosities ranged from 0 to 0.852 and 0.036 to 0.901, respectively. • Conclusions: These new microsatellite markers will be useful in studies of genetic diversity, population differentiation, and gene flow across habitat types in P. subserratum. © 2012 Botanical Society of America.
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