Abstract The snapdragon Antirrhinum majus has been a model species for genetics, plant development, and evolution since the 19th century. Recent studies have expanded the focus to the entire Antirrhinum genus as a model system for rapid evolution (26 species in < 5 million years). However, in-depth studies to reconstruct microevolution in additional snapdragon species are lacking. This study aimed to explore to what extent potential pollinators, flower colour morphs, spatial and environmental factors contribute to differentiation in a small population of the Mediterranean A. charidemi (south-eastern Spain). We studied a population of approximately 200 A. charidemi individuals with either pink or white corollas, characterized by strong topographic heterogeneity (horizontal extension of 120 × 80 meters; 40-meter altitude difference) and diversity in environmental factors (substrate, vegetation). The study analysed pollinator preference for either white or pink corollas, genetic diversity using 13 nuclear SSR loci and three plastid haplotypes, and the spatial population structure. Flower visitors displayed some indication of preference for pink corollas (five of ten bee species) and flower colour morphs were genetically differentiated. However, the strongest pattern of genetic differentiation was associated with a fine-scale spatio-topographic isolation in the population, with five topo-genetic subpopulations and a pollen-to-seed dispersal distance ratio of 4.32. Our results agree with similar patterns of strong spatial genetic isolation found in A. charidemi at larger scales: phylogeographic differentiation of populations and phylogenetic relationships within a south-eastern Iberian Antirrhinum clade. Despite the extreme corolla specialization for bee pollination, spatial isolation appears to be the predominant factor driving short- and long-term differentiation in A. charidemi. We argue that a comprehensive understanding of early stages of rapid evolution requires detailed investigation of fine-scale evolutionary drivers, including both spatial isolation (topography) and ecological factors (e.g. pollination fauna).