We used 13 microsatellite marker loci to determine the genetic diversity of cassava (Manihot esculenta Crantz) grown in home gardens in two Chibchan Amerindian reserves in Costa Rica. We compared the levels of genetic diversity in the reserves with that of commercial varieties typically cultivated in Costa Rica. We found high levels of genetic diversity among cassava plants. Overall, 12 of the 13 loci examined were polymorphic in each Amerindian reserve (P = 92.3). Moreover, we found 36 alleles in the Coto Brus Reserve and 33 in the Talamanca Reserve. In the commercial varieties only nine loci were polymorphic (P = 69.2), and we only found 23 alleles. Heterozygosity was high for all groups of cassava (Coto Brus, Talamanca, and commercial varieties), but it was higher among the commercial varieties. The levels of heterozygosity and allele diversity indicate that there is significant genetic diversity in the home gardens that we examined. Another indication of the high diversity found in these gardens is the number of distinct multilocus genotypes, 28 at Coto Brus and 19 at Talamanca. There was also more than one distinct multilocus genotype found within the commercial varieties, as three were found in Valencia and four in Manyi. Our data also revealed low levels of genetic differentiation between the three groups of cassava (Fst = 0.03), and Nei's genetic distances ranged from 0.0167 to 0.0343. In addition, F estimates (Fis and Fit) indicate excess heterozygotes, both at the subpopulation and the population level. A hierarchical analysis of the genetic variation revealed that variation between sampling locations within each of the three groups of cassava was larger than that between groups (Theta S = 0.0775 and Theta P = 0.0204, respectively). The variety Manyi was the group genetically most distant from all others. We discuss the consequences of these findings for in situ conservation of genetic resources.