Microsatellite data for the six Central European stickleback samples analyzed in the paper "Constraints on speciation suggested by comparing lake-stream stickleback divergence across two continents" (Berner et al. 2010, Molecular Ecology), provided as tab-delimited text file "microcatellite data Berner et al. 2010.txt". The first three columns give the specimen IDs as well as the sample site and watershed codes following the nomenclature used in the publication. Subsequent columns give the length of each allele for each of the six Stn-microsatellite markers. Missing data are coded as "999".