These files provide the raw data necessary to repeat the analyses presented in Sloan &amp; Simmons, Divergence in the internal genital morphology of females correlated with divergence in male intromittent structures among populations of a millipede. Evolution, 2023. IDs Individuals are labelled by their geographic origin: Gingin, Avon Valley, Nalya Park, Kings Park (both KPJ and Thomas Road), Ellis Brook, Beeliar and Serpentine (e.g. Avon1_m is male 1 collected from Avon valley. Morphology PLY (polygon file format) files are the surface mesh files extracted from Avizo v9.2.0. Each .ply file contains the 3D scan data (x, y, z coordinates) that describe the surface mesh for each male gonopod and each female receptaculum. These files can be entered into the Generalized Procrustes Surface Analysis (GPSA) software available in Pomidor et al. (2016) to reproduce the shape variables provided in the  gpsa_ordination_projection files. The .ply files can also be opened in any graphics package to visualize the surface mesh for each individual. The gpsa_ordination files contain the data used in downstream analyses. The columns, Axis1 – Axis<sub>i</sub> are the scores of each individual on the first to ith major axis from the principal coordinates analysis.  Collum area is also provided for each individual. Genetics Two files are provided;  the raw SNP data from DArT, and the set of neutral SNP loci following outlier detection. Cells in this file containing NA represent SNPs that could not be scored. Pomidor B.J., Makedonska J., Slice D.E. 2016 A landmark-free method for three-dimensional shape analysis. PLOS ONE 11(3), e0150368. (doi:10.1371/journal.pone.0150368).