The young leaves are the main source of nucleic acids for population genetic studies in palm-trees; however, the access to this tissue may be limited by specific features of each species. Using root tissues as an alternative source of nucleic acids could facilitate the sampling in large populations. This study tests root tissue viability as an alternative nucleic acids source (root vs. leaf) and explores different protocols (tissue storage and DNA purification methods) to obtain high-quality DNA samples. The results showed no significant differences in DNA concentration and quality for the comparisons of tissue source (leaf vs. root) and DNA purification method (manual vs. kit). For tissue storage method, DNA concentration was significantly higher for root tissues stored in 70% and 90% alcohol solutions versus those obtained from leaf tissue, however for the quality parameters, no differences were found. Results showed the effective potential of using root tissue as an alternative source for nucleic acids, which could facilitate populations sampling of palm-tree species for future studies and this methodological alternative could be applied to other plant systems with similar sampling challenges.