ABSTRACT The genus Manihot Mill. contains about 120 species of which about 104 occur in Brazil. We tested the cross-amplification of ten microsatellite markers developed for Manihot esculenta in 15 species of Manihot endemic to the Brazilian Cerrado. We also evaluated the genetic diversity of Manihot irwinii, M. orbicularis, and M. purpureocostata. Ten pairs of primers were amplified among 14 species of Manihot. The percentage of polymorphic loci per species varied from 70 to 100 %. Nine markers showed amplification and polymorphism when evaluated on polyacrylamide gel. The markers were combined to form three sets for multiplex genotyping for genetic diversity analysis, and showed 51, 75, and 75 alleles in M. irwinii, M. orbicularis, and M. purpureocostata, respectively. The levels of genetic diversity for the transferred markers were high for the three species and proved to be useful for population genetics studies of species of Manihot endemic to the Cerrado. The results of this study will help to better understand the genetic diversity, taxonomy and relationships among species Manihot, and to develop conservation programs for the genus.