The demography of the Andean Puya hamata has been linked to fire regimes and hummingbird behaviour, which might modify the plant’s population genetic diversity. Naturally poor dispersal results in patches of genetically related plants, a pattern intensified further by burning which promotes seedling germination around parent plants. Later, when these plants flower, large patches are attractive to territorial hummingbirds which prevent visits by traplining hummingbird species, carrying pollen from likely unrelated plants. To explore this hypothesis, a genetic study of P. hamata using microsatellite markers was conducted with (i) isolated and grouped adults in two size categories of patches, and (ii) seeds collected from the same patches and isolated individuals. Isolated individual plants were most genetically diverse with close to zero endogamy. Adult plants from large patches showed, lower diversity and higher endogamy than plants from other spatial contexts. Seed genetic structure displayed a gradient of diversity: lower at patch centres but higher at patch edges, in small patches and for isolated infructescences. The spatial context of these plants, especially the contrast between large patch centres and other situations, determines the genetic diversity of their seeds via hummingbird foraging behaviour. Territorial hummingbirds restrict gene flow in and out of large patches, but traplining hummingbirds maintain genetic diversity among isolated plants, small patches and plants at the edges of large patches. Our study illustrates the need to consider interactions between land use, plants and their pollinators when considering genetic diversity at the landscape scale.