This data set comprises simulated and empirical genetic data and associated metadata that were analyzed for the publication "Quantitative Analyses of Coupling in Hybrid Zones" (doi:10.1101/cshperspect.a041434). The data set includes two compressed directories (tar.gz files). dfuseSims.tar.gz contains the simulated data. These are the main (.main) output files from the program dfuse. The simulation conditions are encoded in the file names, this includes the number of demes (number after d), the number of loci (number after L), theta (number after theta) and the replicate number (number after rep). The genetic map size (M) is given if not 1 and the migration rate (m) is given if not 0.1. The directory includes 2250 simulated data sets. data.tar.gz contains the empirical data sets re-analyzed for this paper. We specifically include the final input files needed for analysis. The file formats vary slightly but are described in detail in the supplemental material for the publication and in the R scripts used for analysis. The latter are available from GitHub (https://github.com/zgompert/ClineCoupling). There is one directory per data set within the main compressed directory.