Plant facilitation is a positive interaction where a nurse or nurse plant community alters the local conditions, improving the life-time fitness of other beneficiary plants. In stressful environments, a common consequence is the formation of discrete vegetation patches under nurse plants, surrounded by open space. The consequences of such spatial patterns have been studied mostly at the community level. At the population level, facilitation causes a distribution of beneficiary individuals that could have intra-specific genetic consequences. The spatial patchiness and the increase in local aggregation can potentially affect the population fine-scale genetic structure. In addition, marked microenvironmental differences under nurses versus outside could lead to plastic phenotypic variation between facilitated and non-facilitated individuals, as for example reproductive asynchrony, potentially producing assortative mating. This study tests the hypothesis that plant facilitation can have genetic consequences for the population of a beneficiary plant (Euphorbia nicaeensis) by affecting its spatial genetic structure and mating patterns between subpopulations of facilitated and non-facilitated individuals. Facilitation in this system creates an aggregated distribution of beneficiary individuals compared to a minority of non-facilitated individuals that grow on the open ground. Facilitation also leads to slight phenological differences mediated by strong microenvironmental differences created by nurses compared to the open ground. Yet a molecular analysis showed that, although there is fine scale spatial genetic structure in this system, there is no evidence that it is caused by facilitation. Numerical simulations further showed that spatial genetic patterns in the population are little influenced by the phenological mismatch observed in the field. Synthesis. Facilitation leads to the strong spatial aggregation of beneficiary plants and desynchronizes their flowering phenology, but the magnitude of these effects is not enough to have local genetic consequences in our study system. Facilitation seems thus to have a homogenizing role by allowing the persistence of a diverse gene pool in populations in harsh environments, rather than fomenting genetic differentiation. Further information on other systems where facilitation produces stronger spatial or phenological effects on facilitated plants is needed to fill the large knowledge gap we have on the genetic effects of facilitation.