PATHMATRIX is a tool used to compute matrices of effective geographical distances among samples using a least-cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. Punctual locations (e.g. individuals) or zones encompassing sample data points (e.g. demes) are used in conjunction with a species-specific friction map representing the cost of movement through the land- scape. Matrices of effective distances can then be exported to population genetic software to test, for example, for isolation by distance. PATHMATRIX is an extension to the geographical information system (GIS) software ARCVIEW 3.x.