On the Indonesian island of Flores, populations of tiny humans arose twice, independently and separated by tens of thousands of years, according to new research. The findings offer novel insights into the complex biogeographical and evolutionary history of modern humans in Island Southeast Asia. Flores Island has long been inhabited by short humans, including Homo floresiensis, an ancient species of tiny hominin, which has an unknown relationship to modern humans. Additionally, the island is currently home to a population of pygmy humans, who live near the cave in which H. floresiensis was found. To better understand the short-statured evolutionary history of the humans on Flores, Serena Tucci and colleagues turned to the genetics of Flores pygmies. The authors collected and analyzed the DNA of 32 contemporary pygmy humans, which included 10 whole-genome sequences, and studied their genetic variation. The genomic analysis reveals a complex genetic history showing that modern pygmies have both Neanderthal and Denisovan (another archaic human species) ancestry. However, the authors found no evidence of gene flow with other archaic hominins. Furthermore, Tucci et al. show that the short-stature phenotype of the Flores pygmies is a product of recent polygenic selection on standing genetic variation, rather than genetic heritage. Combined, the authors demonstrate that the modern pygmies of Flores Island are not the descendants of H. floresiensis, which suggests that the insular dwarfism which characterizes both populations arose twice and in at least two separate hominin lineages.