Understanding genetic diversity is crucial for plant adaptation in a changing world. High neutral genetic variation (NGD) can indicate potential for adaptation, informing conservation efforts. Brazil, a megadiverse nation with diverse forests encompassing a great variety of ecosystems, harbours a wealth of plant life, yet studies on NGD remain scarce. This work analyses published data (2001-2022) on NGD in native Brazilian plant populations. We identified 651 studies through a systematic search on the Scopus database, with most using microsatellite markers (SSR; N = 340) and focusing on Fabaceae, Bromeliaceae, and Arecaceae families (N = 107, 72 and 66 respectively). Interestingly, the highly informative SNP markers were underutilized (N = 19), and many papers used dominant markers such as ISSR and RAPD (N = 97 and 62, respectively). This suggests a shift towards next-generation sequencing technologies for a more comprehensive picture of genetic variation. Species-wise, Euterpe edulis Mart. (heart of palm tree) and Hancornia speciosa Gomes (umbu tree) were most studied, highlighting the link between NGD research and economically important or threatened species. Notably, trees and herbs dominated the studies (N = 371 and 194, respectively), with a focus on the Atlantic Forest biome. However, Cerrado and Amazon biomes were also well represented, underscoring the importance of broader investigation across all Brazilian ecosystems. These findings reveal a critical gap in knowledge. With looming climate and landscape changes, a more comprehensive understanding of NGD across Brazil's diverse flora is vital. Future steps include incorporating recent data and performing a meta-analysis to gain deeper insights into national conservation strategies, ultimately aiding in the development of effective strategies to safeguard Brazil's irreplaceable plant biodiversity.