Population genetic data is often essential to inform conservation management. Understanding the distribution of genetic variants within and between populations can reveal novel insights into genetic connectivity and evolutionary processes. However, obtaining such data using invasive approaches such as tissue sampling may negatively affect the very species we are seeking to protect. Thus, interest in using non-invasive environmental DNA (eDNA) techniques for identifying genetic variation within target species populations has grown. Along with this interest comes the desire to expand the amount of population genetic information that can be obtained from eDNA to increasingly large fragments of the genome, such as entire mitogenomes. Here, we introduce an eDNA hybridisation capture approach to sequencing complete mitochondrial genomes of New Zealand fur seals (Arctocephalus forsteri) (Māori: kekeno) from marine water samples. We show that our approach can recover up to 99% of the fur seal mitogenome. Furthermore, we present a pipeline to extract haplotype diversity from such eDNA population genetic data. Haplotypic variation identified using this approach matches previously identified patterns of intraspecific genetic variation from fur seal tissue samples, suggesting that eDNA methods can accurately identify mitochondrial variation. Our study demonstrates that whole mitogenomes can be recovered using hybridisation capture enrichment of eDNA and indicates that eDNA may be a promising tool for population genetics. Within this context, we discuss some of the key challenges that must be overcome before the promise of eDNA can be fully realized.