Dioon caputoi is a long-lived cycad known from only four populations that range in size from 50 to 120, mostly adult individuals. Dioon caputoi has the most narrow geographical range of all Dioon spp. (less than 10 km), existing completely within the boundaries of the Tehuacán–Cuicatlán Biosphere Reserve, Mexico. Negative inbreeding values were found in all four populations (FIT = −0.242) and within subpopulations (FIS = −0.379). Only c. 10% of the total genetic variation was partitioned among populations (FST = 0.099). We also found that most mean values of genetic variation (A = 1.91 ± 0.12; P = 78.9 ± 10.2; HE = 0.35 ± 0.01) are within the range reported for other Dioon species with larger populations and with wider geographical ranges. These results support recent findings that rare plant species maintain high levels of genetic diversity. The heterozygote excess found at all loci is discussed in detail from a neutral evolutionary perspective, leaving arguments as working hypotheses for further research. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 436–447.