The Iberian Peninsula has been described as a glacial refugium for numerous organisms. In particular, there is evidence both from pollen records and genetic studies that shows the existence of Mediterranean conifers (Pinus halepensis Miller, Pinus pinaster Aiton, and Pinus pinea L) in southeastern Spain during the last glacial stage. Data from eight polymorphic allozyme markers were used to study the spatial genetic structure of 11 native populations of maritime pine, P. pinaster, in this region. Models of isolation by distance were adjusted to different groups of populations to test specific hypotheses about the role of mountain ranges in shaping the spatial genetic structure of maritime pine in southeastern Spain. In addition, pairwise gene interchange was analyzed using migration matrix models and maximum likelihood methods to make joint estimates of dispersal rates and population sizes. A complex pattern in the distribution of gene diversity was found, involving historical isolation due to geographical variables for particular populations. The role of mountain ranges in glacial refugia i) reducing the risk of a population bottleneck by altitudinal migration in response to climatic change, and ii) acting as geographical barriers to gene flow, is discussed.