Rafflesia lagascae is a rare endo-holoparasitic species with a disjunct distribution on Luzon Island. It is morphologically very similar to R. manillana from nearby Samar. This study aims to contribute to the taxonomy and conservation of R. lagascae and R. manillana (i.e. the R. lagascae complex) by resolving their patterns of genetic diversity and structure. The results of analyses of a microsatellite data set indicate that despite their frequently extremely small sizes and geographic isolation, Rafflesia populations display moderate genetic diversity and do not show evidence of pronounced inbreeding. Most populations appear to have limited gene flow among them. Patterns of genetic diversity of staminate and pistillate Rafflesia flowers growing on the same Tetrastigma host plants indicate that the R. lagascae complex is monoecious and that host plants are regularly infected by multiple Rafflesia plants. PCoA and Bayesian cluster analyses show that the complex is composed of three genetically isolated taxa. One of these constitutes R. manillana, supporting the morphology-based hypothesis that it is taxonomically distinct from R. lagascae. The second taxon in this complex is composed of a morphologically cryptic R. lagascae population from Mt. Labo, which is genetically distinct from all remaining R. lagascae populations that were studied and that form the third taxon. We recommend that these three taxa are managed as different conservation entities.