Springer-Verlag 2010 Abstract Allozyme diversity and population genetic structure studies were conducted in populations of two Mexican cycad species occurring in adjacent and closely related biogeographic regions. We evaluated if rarity traits in Dioon caputoi, a micro-endemic species, and Dioon merolae, a regional endemic with a wider distribution, influence levels of genetic diversity in different ways. We also explored if genetic structure differs in these species, considering that they have similar population histories. Our results indicate that D. caputoi harbors lower levels of genetic diversity and allelic richness (HE = 0.358, P = 76.9, Ar = 1.86) than D. merolae (HE = 0.446, P = 92.3, Ar = 2). However, genetic structure does not differ between the two species despite their contrasting geographic distributions (FST = 0.06 vs. 0.07; D. caputoi and D. merolae, respec- tively). The comparison of population genetic structure information with historical and geographical aspects of the populations suggests that the rarity of D. caputoi might be due to relatively recent local ecological factors.