Rafflesia species (Rafflesiaceae) are among the flagship plants of South-East Asian countries in which they occur. Three species of Rafflesia, i.e. Rafflesia patma, R. rochussenii, and R. zollingeriana, are known from Java, Indonesia. All three species are threatened with extinction due to human activities that cause habitat loss and fragmentation. Conservation efforts such as determining conservation units for prioritization of those species have been difficult due to the lack of data on their population genetics. Availability of genetic information is important to develop appropriate conservation measures. Our study evaluates genetic diversity and structure of the three Rafflesia species using a total of 166 samples across the island. We used single nucleotide polymorphism (SNP) markers obtained via MIG-seq. The three species of Rafflesia in Java bear much lower genetic diversity compared to what was previously shown for R. speciosa and R. lagascae on Borneo, the Philippines and the Malayan Peninsula. Low genetic diversity within the Javanese Rafflesia species, particularly in R. patma and R. zollingeriana, is attributed to bottleneck events and population expansion in the past. We also provide evidence of clonality and existence of different genotypes within Tetrastigma host plants in two species of Rafflesia. Scattered and fragmented populations as reconstructed in the genetic structure analyses are important to be considered in designing appropriate conservation strategies. Furthermore, we demonstrate how the establishment of Rafflesia ex-situ collections can conserve genetic diversity that may no longer be present in nature and could be used in future reintroduction programs.