The Geographic Distance Matrix Generator is a platform-independent Java application that implements the same powerful suite of spherical functions as the Perpendicular Distance Calculator to compute all pair wise distances from a simple list of geographic coordinates. The Geographic Distance Matrix Generator implements methods founded in spherical geometry because calculations can be performed directly with geographic coordinates, i.e., latitude and longitude, saving researchers time and money by eliminating the need for complex, expensive spatial software. In the fields of phylogeography and landscape genetics, biologists attempt to detect patterns in the distribution of genetic variation across different spatial scales. The most commonly known process is isolation by distance (IBD), under which genetic similarity decreases with geographic distance. Barriers to migration of organisms can hinder gene flow, thus increasing genetic distance, even if populations are not far apart. With the increasing availability of mobile GPS technology, every scientist can obtain latitude-longitude coordinates for target organisms, which can later be used in regression analyses in conjunction with genetic distances, or matrix associations with permutations for statistical testing, as well as multiple matrix correlations when testing for more complex biogeographic and ecological scenarios (Mantel and partial Mantel tests, respectively).The Geographic Distance Matrix Generator can be used to easily generate distance matrices needed for these types of analyses.