In Myrtaceae and Rosaceae species, the transferability of microsatellite markers has been extensively explored and proven effective [19,50–53]. This approach has facilitated and accelerated the availability of molecular genetic data for species in absence of their own microsatellite markers. Therefore, it was predicted that the Asteraceae microsatellite primers could be useful in characterizing the A. flaccida populations; however, although Asteraceae primers were selected from the literature based on phylogenetic proximity, reports of transferability, and numbers of amplified alleles, they were not transferrable to A. flaccida. It is interesting that when these microsatellite primers were tested in 10 samples, 66.66% amplified fragments of expected size; however, when they were evaluated in whole populations, these primers were monomorphic and/or had a high number of null alleles. Notably, in the majority of studies that developed microsatellite primers, the authors tested these primers on a small number of samples from other species, which may falsely confirm their transferability. As with A. flaccida, these primers may have an excess of null alleles and/or be monomorphic when evaluated in populations with higher numbers of individuals and therefore, are not useful in population genetic studies. The results obtained in this study reinforce the need for the development of microsatellite primers specific to A. flaccida. As the development of microsatellites is expensive, and our group has been developing works with ISSR markers, we used these markers to get faster and more economical population genetic data of A. flaccida.