Microsatellites or simple sequence repeats (SSRs) are useful molecular markers allowing for efficient conservation and sustainable use of genetic resources of plant species. Development of SSR marker system for new species is a very expensive task and time consuming. Cross-species amplification of microsatellite loci is considered as a cost-effective approach for developing microsatellite markers for new species. The aim of this work was to examine the transferability of some SSR markers of two Arecaceae species (Astrocaryum aculeatum and Elaeis oleifera), in Acrocomia aculeata. Out of the total markers analysed 44% of the markers successfully amplified the genomic DNA in A. aculeata, of which 26% were polymorphic detecting a range of three to eight alleles with an average of 4.5 per locus. High average percentage of polymorphic loci (P= 71.2%) per provenance was obtained within a range of 57–100% detecting genetic variation in A. aculeata germplasm collections. The polymorphic markers detected a positive inbreeding coefficient (F>0) per locus revealing heterozygote deficiency in the accessions that were analysed. As the cross-amplification was at family level, in which the taxonomic distance is relatively wider between the sources (A. aculeatum and E. oleifera) and the target (A. aculeata) species, the amplification success was relatively low. However, the results are promising and implicated that high cross-amplification success could be achieved at species or genus level in A. aculeata. The markers will contribute towards the domestication of the potential macaw palm through realizing various studies such as population genetics, germplasm characterization, genetic improvement and conservation.