Repeat blocks, microsatellites or simple sequence repeats (SSRs) can produce good co-dominant molecular markers for genetic diversity analysis and the determination of self-pollination rates in progenies originating from open pollination of selected genotypes. The enrichment of guarana genomic libraries was underway when it was confirmed that we are working with a complex polyploid species with 210 chromosomes. The probes (CA)₁₂, (CT)₁₂ and (TC)₁₄ were used to finish the enrichment of four libraries for repeat blocks and the screening of a databank of expressed sequence tags (ESTs) from guarana seeded-fruits was accomplished as well. Fifteen clonal cultivars were genotyped with three replicas at 10 out of 27 identified loci using the 59 alleles that passed the reproducibility criterion. A large number of short repeat blocks were identified and this was considered to be a consequence of the recent polyploidization event. However, blocks with eight or more repeats ideal for genotyping were scarce. Annealing of most probes to short blocks by partial complementarity could explain the scarcity of longer blocks in genomic libraries but cannot explain why they were rare in the ESTs. Due to the complexity of the genotypes, alleles were treated as dominant traits. ESTs harboring repeat blocks had the functional annotation renewed. Locus GRN07 is inserted in a homologue of the MOTHER OF FLOWERING LOCUS T AND TFL1 (MFT), in which 3’-UTR displays clear post-transcriptional regulatory features. MFT and its variants are probably involved in the determination of seed germination and embryo growth characteristics. Other accessed loci can be involved in plant architecture and defense reactions. It was concluded that the alleles described in the present work can be used to distinguish guarana cultivars and possibly to analyze segregation using the progenies of controlled pollinations between divergent genitors. Also, the fingerprints obtained can be added to the morphological and agronomic descriptors of the cultivars.