Duckweeds, including the common duckweed Lemna minor, are increasingly used to test eco‐evolutionary theories. Yet, despite its popularity and near‐global distribution, the understanding of its population structure (and genetic variation therein) is still limited. It is essential that this is resolved, because of the impact genetic diversity has on experimental responses and scientific understanding. Through whole‐genome sequencing, we assessed the genetic diversity and population genomic structure of 23 natural Lemna spp. populations from their natural range in Switzerland. We used two distinct analytical approaches, a reference‐free kmer approach and the classical reference‐based one. Two genetic clusters were identified across the described species distribution of L. minor, surprisingly corresponding to species‐level divisions. The first cluster contained the targeted L. minor individuals and the second contained individuals from a cryptic species: Lemna japonica. Within the L. minor cluster, we identified a well‐defined population structure with little intra‐population genetic diversity (i.e., within ponds) but high inter‐population diversity (i.e., between ponds). In L. japonica, the population structure was significantly weaker and genetic variation between a subset of populations was as low as within populations. This study revealed that L. japonica is more widespread than previously thought. Our findings signify that thorough genotype‐to‐phenotype analyses are needed in duckweed experimental ecology and evolution.