Data and code used in bioinformatic processing, bathymetry calculations, population genetic analyses and their output files. Ultraconserved Elements (UCEs) were sequenced in 68 individuals of leafy seadragons (Phycodurus eques, Syngnathidae) sampled across their range along the southern Australian coast. The repository contains A) Scripts to process the sequence data and the resulting BAM read mapping files VCF files with SNPs before and after filtering B) Scripts, input files, and output files for the analyses to reconstruct shallow water areas at different sea levels estimate population structure (PCA, DAPC, Structure, SVDquartets), and spatial genetic patterns (IBD plots, EEMS) calculate genetic diversity (individual-level heterozygosity, population-level heterozygosity, Tajima's D) perform phylogeographic modeling (DIYABC).