Environmental DNA (eDNA) has enabled novel pathways to explore questions around population genetics. eDNA is non-invasive, holding potential for sampling from endangered, cryptic, or elusive species, where traditional methods (e.g. biopsy) can be more challenging. Using water samples collected from the fluke print of Hector’s dolphin (Cephalorhynchus hectori hectori), an endemic, endangered and culturally important (taonga) species, we explored the efficacy of eDNA to understand population structure. Over two summers, we collected 133 water samples across three areas on the east coast of Aotearoa New Zealand’s South Island: Banks Peninsula (n=79), Timaru (n=39) and Dunedin (n=15). We targeted a 348bp region of mitochondrial DNA (mtDNA) through qPCR and IlluminaTM sequencing, successfully detecting Cephalorhynchus DNA in 87 water samples. We identified nine haplotypes across our study area, including one novel haplotype. Occurrence and haplotype frequencies in Banks Peninsula and Timaru matched well with previous tissue-based studies and were similar to other East Coast South Island subpopulations. In Dunedin, however, our results suggest a closer relationship to South Coast populations, which has implications for how dolphins here are managed. Ultimately, we show that eDNA sampling can be used to elucidate matrilineal population structure for the Hector’s dolphin.