Environmental DNA (eDNA) sampling uses genetic material in the environment to infer species presence sight-unseen. The method has rapidly become a powerful tool for monitoring biodiversity. However, biological diversity, as per the Convention on Biological Diversity definition of “diversity within species, between species and of ecosystems” is more inclusive than most eDNA studies cover: The vast majority focus only on between-species and ecosystem-level biodiversity. However, a tantalizing prospect, as illustrated by Farrell et al. (2022) in this issue of Molecular Ecology Resources, is that we might also be able to unlock information about individual and population-level diversity via population genomic analysis of these environmental samples. Farrell et al. (2022) found that targeted samples of beach sand contained genetic material not just informative about sea turtle presence, but also indicated the presence of pathogens and genome-wide mitochondrial and nuclear sequences that could accurately infer individual turtle source population. Moving from proof-of- concept to robust, population genomic inference will require a growth of genomic resources for nonmodel organisms and careful study design considerations, some of which have already been pioneered by related fields.