This study concerns spatial genetic patterning, seed flow and the impact of modern varieties in maize populations in Chimaltenango, Guatemala. It uses a collection of 79 maize seed samples from farmers in the area and five samples derived from modern varieties. Bulked SSR markers employed with bulked samples (ten plants) were used. Genetic distances between populations based on these SSR data were used as a measure of co-ancestry. The study describes the genetic variation in space, assesses the association of maize diversity with spatial and environmental descriptors and quantitative traits, and provides a test of the impact of improved varieties. Maize diversity showed significant isolation-by-distance locally, but not regionally. This was interpreted as evidence for a difference between local and regional mechanisms of seed exchange; regional exchange is more related to innovation. There was also a significant association with altitude and ear/grain characteristics (related to racial classifications). Also, consistent evidence for the influence of modern varieties of maize was found, although its impact was limited spatially. It is argued that the spatial distributions of maize diversity are important to consider for germplasm collection, but should be seen as a recent outcome of dynamic processes.