Magnolias are representative shrub and tree species of the Tropical Montane Cloud Forest (TMCF) in Mexico, which is one of the most endangered ecosystems due to anthropogenic landscape degradation and climate change. Magnolia schiedeana is a vulnerable and restricted endemic TMCF species, occurring in scattered TMCF fragments in the Sierra Madre Oriental. In this study, we investigated spatial patterns of genetic diversity across the M. schiedeana species range and assessed whether gene flow was influenced by topographic and environmental factors. We sampled eleven remnant populations across the species range and genotyped 180 individuals at eight nuclear microsatellite loci. Our data showed a strong spatial structure in five genetic clusters, which match the patchy geographic distribution of M. schiedeana. Contemporary migration rates between these genetic clusters were very low. Levels of genetic diversity within populations were moderate to high, and no evidence of inbreeding was found. Our results from landscape genetic analysis showed that isolation by distance, rather than topography or environmental variation, was the main process shaping genetic differentiation. Urgent actions are needed to protect M. schiedeana populations as most of them persist isolated within agricultural and urban landscapes. Ex-situ management actions would be crucial to ensure the conservation of genetically diverse germplasm for the in-situ propagation where it has gone locally extinct.