Random amplified polymorphic DNA (RAPD) markers were used to study the spatial genetic structure in two populations (Bolarque and Entrepeñas) of endangered cliff specialist Antirrhinum microphyllum Rothm. (Scrophulariaceae). Mantel tests found no significant linear correlations between geographic and genetic data. However, redundancy analysis (RDA) models developed using the spatial data as the constraining matrix were highly significant, and spatial data explained 13.6% and 11.1% of total genetic variation in Bolarque and Entrepeñas, respectively. Moran's I correlograms and Mantel correlograms revealed a positive autocorrelation in the first distance class (15 m), which suggests a patchy distribution of genetic diversity. This distribution is consistent with the genetic vicinities that are expected from the territorial behavior of main pollinator Rhodanthidium sticticum (Megachilidae), the predominant short-distance seed dispersal, and the patchy spatial distribution of available safe sites. The gradient pattern obtained in Entrepeñas was consistent with standard isolation-by-distance models. However, a differential sinusoidal pattern was obtained in Bolarque, which would indicate a more frequent gene flow between patches and might be due to lower plant density there. The spatial genetic structure coexists with a strict self-incompatibility system in the species. Simplified RDA models obtained using a stepwise forward selection comprised the easting component in Entrepeñas and the easting and northing components in Bolarque. Similar results were obtained with directional correlograms. These differential patterns can be explained by the distinct spatial arrangement of the populations (linear and bidimensional in Entrepeñas and Bolarque, respectively).