SPASSIGN and SPAIDA are two small programs useful to detect isolate by distance of microsatellite loci. The programs are written in C and are available for Linux and Windows system at http://www.hi.is/~snaebj/programs. html. SPAIDA calculates two estimates of spatial autocorrelation, Moran's I and Geary's c, first by assuming the infinite allele model, and second by assuming a stepwise mutational model. SPASSIGN calculates the assignment probabilities of an individuals genotype to the location where it was sampled and compares probabilities of assignment to other locations. Genetic distances among regions based on the overall differences in likelihoods are calculated.