Manioc, Manihot esculenta, is economically important in many tropical and subtropical countries. The genetic variability of the species has not been fully explored, and new information may help expand its use. Molecular markers based on retrotransposons have good potential for analysis of genetic diversity given their abundance in the genome. Eight long terminal repeat retrotransposons were selected for the development of inter-retrotransposon-amplified polymorphism markers. To test these primers, we analyzed 32 varieties from Anori, 30 from Manicoré and 10 Mandiocabas from the Manioc Germplasm Bank at Embrapa Western Amazonia. The six informative primer pairs yielded 20- 60 polymorphic bands, averaging 92% polymorphism (51.7-98.4) and 0.37 heterozygosity (0.17 to 0.40), with a Shannon information index of 0.54 (0.26-0.59). These markers can be used to explore the genetic diversity of manioc.