Mahogany, Swietenia macrophylla (Meliaceae) is the most valuable hardwood species in Neotropics and is seriously threatened owing to over-exploitation and habitat destruction. The population genetic structure and mating system of S. macrophylla were studied in the Brazilian Amazon for conservation purposes. Ten highly polymorphic micro satellite markers were developed from an enriched genomic library of S. macrophylla and combined in three multiplexed fluorescence based genotyping systems. The number of alleles per locus ranged from 11 to 25 (mean = 15.8). The probability of genetic identity (7x10- 15) and the probability of paternity exclusion (0.999998) found over all loci indicate the high discriminating power of these markers. The genetic structure was investigated in seven populations 8- 2,103 km apart. High genetic diversity was detected within populations (mean He = 0.761, range 0.719-0.800) and a significant level of inbreeding was found (f = 0.046, P<0.0001, range 0.014-0.097) indicating nonrandom mating of individuals within populations. Genetic differentiation among populations was significant (A = 0.12 and p = 0.14, P<0.0001), but no clear pattern of isolation by distance was found. Conservation strategies for mahogany should take into account the existence of important genetic structuring of populations. S. macrophylla seems to have adaptations that preferentially produce outcrossed progeny but also allows for selfing. The high multilocus outcrossing rate (tm = 0.958) estimated for one population indicated that, although there was a prevalence of outcrossing, selfing was not negligible. Around 4-6% of seedlings in the population were likely to have resulted from self-fertilization and substantial biparental inbreeding was denoted by the significant difference between the multilocus and singlelocus estimates (tm - ts = 0.14). Owing to the species pre-adaptation to colonize newly open, disturbed habitats, many of the remaining trees in logged areas may persist as viable individuals which could be very important for population recovery and genetic conservation programmes.