Comparisons of genetic diversity and population genetic structure among different life history stages provide important information on the effect of the different forces and micro-evolutionary processes that mould diversity and genetic structure after fragmentation. Here we assessed genetic diversity and population genetic structure using 32 allozymic loci in adults, seeds, seedlings and juveniles of eight populations of the micro-endemic shrub Cestrum miradorense in a highly fragmented cloud forest in central–eastern Mexico. We expected that due to its long history or rarity, this species may have endured the negative effects of fragmentation and would show moderate to high levels of genetic diversity. High genetic diversity (He = 0.445 ± 0.03), heterozygote excess (FIT = −0.478 ± 0.034, FIS = −0.578 ± 0.023) and low population differentiation (FST = 0.064 ± 0.011) were found. Seeds had higher genetic diversity (He = 0.467 ± 0.05) than the later stages (overall mean for adults, seedlings and juveniles He = 0.438 ± 0.08). High gene flow was observed despite the fact that the fragmentation process began more than 100 years ago. We conclude that the high genetic diversity was the result of natural selection, which favours heterozygote excess in all stages, coupled with a combination of a reproductive system and seed/pollen dispersal mechanisms that favour gene flow.