The establishment of linkages between habitats is of great importance to avert the detrimental impacts of land fragmentation and climate change on biodiversity. Linkages need to be cost-efficient, and should account for specific dispersal requirements of species. Since cost-efficient linkages defined independently for each individual species are more costly than linkages optimised for multiple species, there is need for methods specifically designed to retrieve efficient linkages for multiple species. MulTyLink (Multiple Type Linkages) is a C++ open source program that defines cost-efficient linkages free of barriers for the species considered, and that allows species-specific dispersal requirements to be considered. Here we present, discuss and illustrate the algorithms used by MulTyLink to identify cost-efficient linkages for multiple species.