This study uses ISSR molecular markers to characterize the demographic pattern, and spatial genetic structure (SGS) at different life stages of development (cohorts) in a natural population of Copernicia prunifera in the Rio Grande do Norte State, Brazil. All individuals were sampled and georeferenced in a 0.55-ha plot. The demographic analyses showed a clustered pattern in the first-distance classes and a random or segregated pattern at higher distance classes for all cohorts. Among the three studied life stages, juveniles showed the greatest value for Nei’s genetic diversity index (HE = 0.369), while the lowest was found among reproductive adults (HE = 0.341). Greater genetic differentiation was found within life stages (98.61%) than among stages (1.39%). The total population (N = 161) showed positive and significant kinship in the first-distance class (12.3 m). The juveniles showed significant kinship up to 10.5 m. Non-reproductive adults had a positive kinship in the first-distance class (11.0 m) and a random distribution of genotypes in the remaining classes, while reproductive adults showed a random spatial distribution of genotypes. Tests for genetic bottleneck showed that the number of loci with excess observed heterozygosity was greater than expected. The SGS results reflected the restricted seed dispersion of the species, and the genetic bottleneck reflected the reduction of genotypes as a result of the anthropization of C. prunifera natural environments.