We studied the levels of genetic diversity of Swietenia macrophylla (big leaf mahogany) in five successional plots in the Santa Rosa National Park, Guanacaste, Costa Rica. We selected sites with different lengths of time since the last major disturbance (typically fire): 6, 9, 15 and 20 years. In addition, we also included a patch of mature forest that had experienced selective logging and other human activity in the past 100 years. Genetic diversity was assessed using five polymorphic DNA microsatellite loci. We found a total of 21 alleles in the five loci examined, in which the number of alleles present varied among the five sites studied. Allelic diversity varied between sites ranging from 20 to 14 alleles, and our data revealed that earlier successional sites have more alleles than older sites. There was significant heterogeneity in allele frequencies between sites; however, genetic differentiation between populations was low (FST = 0.063) indicating that most of the variation was found within sites and extensive gene flow between sites. In addition, our analysis also showed that genetic diversity of adult trees does not solely determine the diversity of seedlings and saplings found around them, also supporting the existence of extensive gene flow. The impact of these findings for the design of conservation strategies for tropical dry forests trees is discussed.