Cedrela fissilis is an endangered timber species associated with seasonal forests throughout South America. We investigated a population of C. fissilis (PAN) located toward central Brazil to uncover insights on how an ecotone may have shaped the evolutionary history of this species at the local scale. PAN consisted of 18 mother trees and their 283 offspring (18 families), which were genotyped with ten microsatellite loci. We supplemented our dataset with equivalent microsatellite data from 175 specimens representing the east and west lineages of C. fissilis. An array of complementary methods assessed PAN for genetic diversity, population structure, and mating system. In PAN, the gene pool of the east lineage combined with a third (previously unidentified) lineage to form an admixture population. PAN is under inbreeding (Ho = 0.80 and 0.74, uHe = 0.85 and 0.82, Ap = 1.1 and 7.1, F = 0.06 and 0.10, for mother trees and offspring, respectively). Mother trees were predominantly outcrossing (tm = 0.95), with some selfing (1 − tm = 0.05), and crossing between related individuals (tm–ts = 0.07); they received pollen from few donors (Nep = 9). Restricted gene flow within PAN gave rise to a strong population structure, which split the 18 families into six groups. Some mother trees were reproductively isolated. Conservation perspectives are discussed.