Raw sequencing reads generated as part of a more detailed investigation into the demographic history and adaptive variation of coastal Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Western Australian waters. We employed a double-digest restriction-site associated DNA sequencing (ddRAD) approach using EcoRI/MseI enzymes to create a genomic SNP dataset. This specific submission includes sequencing data from 54 of the total 133 individuals analyzed in the study MEC-24-0760. The raw read data for the remaining 79 individuals have already been deposited under BioProject ID PRJNA966102. Together, these datasets provide a comprehensive resource for examining population structure, demographic history, and adaptive evolution in these dolphin populations.