Dioscorea transversa, a nutritious edible tuber plant, with pantropical distribution is culturally significant for many Australian Indigenous groups. However, the biology of Australia’s D. transversa is not well known, including the genetics and hypothesized influence of Indigenous harvest patterns. To explore this, the present study focussed on two distinct regions of D. transversa’s range (northeast Arnhem Land and mid coastal New South Wales) and aimed to: 1) document Indigenous cultural knowledge of D. transversa; 2) compare population genetic patterns; and 3) explore how Indigenous knowledge and genetic data could inform combined biological and cultural (biocultural) restoration. Across 17 sites from the two regions, 17,428 single nucleotide polymorphisms were analysed from 174 plants, and nine Indigenous knowledge holders interviewed. Clonality emerged as a genetic signal of contemporary harvest in northeast Arnhem Land, aligning with traditional Yolŋu practice of replanting tuber tops. Here, sites also showed high genetic divergence aligning with translocation cultural protocol, while in New South Wales, low differentiation between sites suggested higher gene flow or recent population expansion aligning with Dharug/Guringai suggestions of past dispersal. New South Wales custodians emphasised cultural loss following colonisation and strong interest in cultural renewal. Overall, this study demonstrated how Indigenous knowledge and genetics could guide specific place-based biocultural restoration actions for D. transversa.